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PDBID Method Resolution Release Date NLP types # NLPs H3 H4 H2A H2B H1 Dna variant Dna length Title Authors DOI Publication H3 taxa H4 taxa H2A taxa H2B taxa H1 taxa Release Year Interactors Interactor categories Interactor UIDS Histone UIDS Q-score
0 9XYC EM 3.50 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 139 Pol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome LEDGF+nucleosome map Q Syau, D., Farnung, L. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 PC4 and SFRS1-interacting protein Histone_methylation_H3K36_reader, Histone PTM readers, Transcription factors, Transcription-associated O75475 P06897, P84233, P62799, P02281 0.356
1 9RN2 EM 4.10 2026-02-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 138 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2 Vecchia, L., Weiss, J., Cavadini, S., Kempf, G., Kater, L., Pathare, G., Thoma, N.H. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Transcription activator BRG1, Actin-like protein 6A, Actin, cytoplasmic 1, N-terminally processed, AT-rich interactive domain-containing protein 1A, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, SWI/SNF complex subunit SMARCC2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1, Zinc finger protein ubi-d4, Green fluorescent protein,POU domain, class 5, transcription factor 1, Transcription factor SOX-2 Cell cycle, Transcription factors, Transcription-associated, Chromatin remodelers, SWI/SNF P51532, O96019, P60709, O14497, Q12824, Q8TAQ2, Q96GM5, Q92785, P42212, P48431 P04908, P68431, P62805, P06899 0.141
2 8PC6 EM 3.04 2023-08-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Histone_methylation_H3K36_reader, Histone PTM readers, Transcription factors, Transcription-associated O75475 P06897, P84233, P62799, P02281 0.484
3 8OTT EM 3.30 2023-05-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 144 MYC-MAX bound to a nucleosome at SHL+5.8 Michael, A.K., Stoos, L., Crosby, P., Eggers, N., Nie, X.Y., Makasheva, K., Minnich, M., Healy, K.L., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, R.S., Andersch, F., Fribourgh, J.L., Schubeler, D., Zuber, J., Liu, A.C., Becker, P.B., Fierz, B., Partch, C.L., Menet, J.S., Thoma, N.H. 10.1038/s41586-023-06282-3 37407816 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Myc proto-oncogene protein, Protein max Transcription factors, Transcription-associated P01106, P61244 P68431, P04908, P62805, Q8CGP7, P06899 0.411
4 8OSJ EM 6.20 2023-05-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 128 Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL-6.2 (DNA conformation 1) Michael, A.K., Stoos, L., Crosby, P., Eggers, N., Nie, X.Y., Makasheva, K., Minnich, M., Healy, K.L., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, R.S., Andersch, F., Fribourgh, J.L., Schubeler, D., Zuber, J., Liu, A.C., Becker, P.B., Fierz, B., Partch, C.L., Menet, J.S., Thoma, N.H. 10.1038/s41586-023-06282-3 37407816 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Circadian locomoter output cycles protein kaput, Basic helix-loop-helix ARNT-like protein 1 Transcription factors, Transcription-associated O08785, Q9WTL8 P04908, P68431, P62805, P06899 0.219
5 8OL1 EM 3.50 2024-02-14 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 cGAS-Nucleosome in complex with SPSB3-ELOBC (composite structure) Xu, P., Liu, Y., Liu, C., Guey, B., Li, L., Melenec, P., Ricci, J., Ablasser, A. 10.1038/s41586-024-07112-w 38418882 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Cyclic GMP-AMP synthase, SPRY domain-containing SOCS box protein 3, Elongin-C, Elongin-B Transcription factors, Transcription-associated, E3 ubiquitin-protein ligation, 2'3'-cGAMP, Synthesis of second messengers, Antiviral defense, DNA repair Q8N884, Q6PJ21, Q15369, Q15370 Q99877, Q96KK5, Q99878, Q71DI3, Q93079, P62805 0.4
6 8JH2 EM 5.70 2023-11-29 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 127 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Akatsu, M., Ehara, H., Kujirai, T., Fujita, R., Ito, T., Osumi, K., Ogasawara, M., Takizawa, Y., Sekine, S.I., Kurumizaka, H. 10.1016/j.jbc.2023.105477 37981206 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.145
7 7ZSB EM 6.60 2022-11-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 219 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. 10.1038/s41594-022-00865-w 36411341 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta Transcription factors, RNA polymerases, Transcription-associated, DNA repair, Euchromatin-associated P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145 P06897, P84233, P62799, P02281 0.277
8 7UND EM 3.00 2022-10-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 131 Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38) Filipovski, M., Soffers, J.H.M., Vos, S.M., Farnung, L. 10.1126/science.abo3851 35709268 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RPOL4c domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, RPB8, RPB9, RPB10, RPB11, RNA polymerase II subunit K, Transcription elongation factor SPT6, Transcription elongation factor A protein 1, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, A0A4X1TVZ5, A0A481DF93, A0A8D1GCS3, A0A4X1VTX4, A0A4X1VEK9, A0A4X1VKG7, A0A4X1TRS6, Q7KZ85, P23193, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 Q6AZJ8, P84233, P62799, P02281 0.216
9 7OHB EM 3.40 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 TBP-nucleosome complex Wang, H., Xiong, L., Cramer, P. 10.1073/pnas.2108859118 34301908 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 TATA-binding protein Transcription factors, Transcription-associated P13393 P06897, P84233, P62799, P02281 0.435
10 7NKX EM 2.90 2021-08-25 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 139 RNA polymerase II-Spt4/5-nucleosome-Chd1 structure Farnung, L., Ochmann, M., Engeholm, M., Cramer, P. 10.1038/s41594-021-00578-6 33846633 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Chromo domain-containing protein 1, Chromatin elongation factor SPT4, Transcription elongation factor SPT5 Transcription-associated, Chromatin remodelers, RNA polymerases, Transcription factors, Centromere-associated, Heterochromatin-associated, CHD, SPT4-SPT5 complex, Euchromatin-associated P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P32657, P32914, P27692 P06897, P84233, P62799, P02281 0.444
11 6J4X EM 4.30 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 127 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.233
12 9R2Q EM 3.20 2025-07-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 142 p53 bound to nucleosome at position SHL-5.7 (non-crosslinked sample) Chakraborty, D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Cellular tumor antigen p53 Transcription-associated, Transcription factors, Cell cycle, DNA repair P04637 P04908, P68431, P62805, P06899 0.361
13 9WMV EM 4.66 2025-12-24 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 168 Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Kujirai, T., Ehara, H., Ito, T., Henmi, M., Oya, E., Kobayashi, T., Sekine, S.I., Kurumizaka, H. 10.1126/sciadv.aed1952 41604494 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Histone-lysine N-methyltransferase, H3 lysine-36 specific, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4QY01, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.168
14 9EGX EM 2.90 2024-12-18 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 159 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-hexasome, bp +27 Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 A0A310TTQ1, P06897, P62799, P02281 0.25
15 8ZJR EM 3.30 2025-08-13 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 131 Structure of nucleosome-bound RFX5 complex Xue, W., Han, Y., Tian, Y., Wang, J., Xie, Z., Zheng, X., Yue, X., Dong, S., Li, H., Luo, Z., Zhang, S., Yang, Y., Zou, Z., Li, W., Ma, N., Zhu, F., Chen, C., Yin, Y., Zhang, Y., Xu, K. 10.1093/nar/gkaf734 40744500 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-binding protein RFX5 Transcription factors P48382 O60814, Q71DI3, P04908, P62805 0.481
16 8VFZ EM 4.10 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 171 Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 2) Zhou, B.R., Feng, H., Huang, F., Zhu, I., Portillo-Ledesma, S., Shi, D., Zaret, K.S., Schlick, T., Landsman, D., Wang, Q., Bai, Y. 10.1016/j.molcel.2024.07.016 39121853 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Hepatocyte nuclear factor 3-alpha Transcription factors, Transcription-associated P55317 P04908, P68431, P62805, P06899 0.27
17 8RBX EM 4.10 2024-02-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 161 Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex Fianu, I., Ochmann, M., Walshe, J.L., Dybkov, O., Cruz, J.N., Urlaub, H., Cramer, P. 10.1038/s41586-024-07269-4 38570683 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription elongation factor SPT5, Integrator complex subunit 1, Integrator complex subunit 2, Integrator complex subunit 4, Integrator complex subunit 5, Integrator complex subunit 6, Integrator complex subunit 7, Integrator complex subunit 8, Integrator complex subunit 9, Integrator complex subunit 10, Integrator complex subunit 11, Integrator complex subunit 13, Integrator complex subunit 14, Integrator complex subunit 15, Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform, Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, DSS1, Negative elongation factor A, NELF-B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B, Negative elongation factor C/D Cell cycle, Transcription factors, Transcription-associated, RNA polymerases, Euchromatin-associated A0A8D1DPV6, Q9H0H0, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A8D0JYF1, O00267, Q8N201, Q96HW7, Q6P9B9, Q9UL03, Q9NVH2, Q75QN2, Q9NV88, Q9NVR2, Q5TA45, Q9NVM9, Q96SY0, Q96N11, P30153, P67775, Q9H3P2, Q8WX92, Q8IXH7 P62805, Q6NXT2, P06899, P0C0S8 0.037
18 7XSE EM 3.60 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 134 RNA polymerase II elongation complex transcribing a nucleosome (EC42) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.238
19 6J50 EM 4.70 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 128 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.195
20 6J4W EM 7.90 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 171 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Spt5 Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, F2QTN1, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.123
21 6YOV EM 3.42 2020-05-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 131 OCT4-SOX2-bound nucleosome - SHL+6 Michael, A.K., Grand, R.S., Isbel, L., Cavadini, S., Kozicka, Z., Kempf, G., Bunker, R.D., Schenk, A.D., Graff-Meyer, A., Pathare, G.R., Weiss, J., Matsumoto, S., Burger, L., Schubeler, D., Thoma, N.H. 10.1126/science.abb0074 32327602 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Green fluorescent protein,POU domain, class 5, transcription factor 1, Transcription factor SOX-2 Transcription factors, Transcription-associated P42212, P48431 P04908, P68431, P62805, P06899 0.35
22 9EH1 EM 3.10 2024-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 170 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerase I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, Superkiller complex protein 8, N-terminally processed, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2 Transcription factors, Histone PTM writers, Transcription-associated, RNA polymerases, Histone_methylation_H3K4_writer, PAF1C, Histone_methylation_H3K36_writer, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A8D1DPV6, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A8W4F9W9, F1RKE4, A0A4X1TRS6, Q96ST2, Q6PD62, Q92541, B7Z4W0, Q9GZS3, A0A2R8YHB3, P63272, Q9BYW2 A0A310TTQ1, P06897, P62799, P02281 0.237
23 8VG2 EM 3.04 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B H1.4 601 196 Cryo-EM structure of FoxA1 and GATA4 in complex with H14 chromatosome Zhou, B.R., Bai, Y. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens 2024 Hepatocyte nuclear factor 3-alpha Transcription factors, Transcription-associated P55317 P68431, P04908, P10412, P62805, P06899 0.493
24 8OSL EM 4.90 2023-05-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 147 Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 2, additional 3D classification and flexible refinement) Michael, A.K., Stoos, L., Crosby, P., Eggers, N., Nie, X.Y., Makasheva, K., Minnich, M., Healy, K.L., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, R.S., Andersch, F., Fribourgh, J.L., Schubeler, D., Zuber, J., Liu, A.C., Becker, P.B., Fierz, B., Partch, C.L., Menet, J.S., Thoma, N.H. 10.1038/s41586-023-06282-3 37407816 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Circadian locomoter output cycles protein kaput, Basic helix-loop-helix ARNT-like protein 1 Transcription factors, Transcription-associated O08785, Q9WTL8 P04908, P68431, P62805, P06899 0.177
25 8OSK EM 3.60 2023-05-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 124 Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map) Michael, A.K., Stoos, L., Crosby, P., Eggers, N., Nie, X.Y., Makasheva, K., Minnich, M., Healy, K.L., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, R.S., Andersch, F., Fribourgh, J.L., Schubeler, D., Zuber, J., Liu, A.C., Becker, P.B., Fierz, B., Partch, C.L., Menet, J.S., Thoma, N.H. 10.1038/s41586-023-06282-3 37407816 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Circadian locomoter output cycles protein kaput, Basic helix-loop-helix ARNT-like protein 1 Transcription factors, Transcription-associated O08785, Q9WTL8 P04908, P68431, P62805, P06899 0.267
26 7OHA EM 2.90 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 122 nucleosome with TBP and TFIIA bound at SHL +2 Wang, H., Xiong, L., Cramer, P. 10.1073/pnas.2108859118 34301908 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 TATA-binding protein, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2 Transcription factors, Transcription-associated P13393, P32773, P32774 P06897, P84233, P62799, P02281 0.516
27 9R2P EM 4.18 2025-07-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 131 p53 bound to nucleosome at position SHL+5.9 (crosslinked sample) Na, N.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Cellular tumor antigen p53 Transcription-associated, Transcription factors, Cell cycle, DNA repair P04637 P04908, P68431, P62805, P06899 0.196
28 9S0U EM 6.72 2025-09-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 175 State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 Walshe, J.L., Ochmann, M., Neef, U., Dybkov, O., Dienemann, C., Oberthur, C., Zheenbekova, A., Urlaub, H., Cramer, P. 10.1038/s41467-025-65439-y 41162378 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription elongation factor SPT6, Histone-lysine N-methyltransferase SETD2, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WD repeat-containing protein 61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit SPT16 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K36_writer, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, FACT, DNA replication, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated, DNA repair A0A8D1DPV6, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A8D1KNW4, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A8D0JYF1, Q7KZ85, Q9BYW2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, Q4R941, O00267, Q9Y5B9 O60814, Q71DI3, P04908, P62805 0.108
29 8HE5 EM 6.95 2023-07-05 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 154 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, DNA repair protein Transcription factors, Transcription-associated, RNA polymerases, DNA repair, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, C4QY79, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R198 P04908, P68431, P62805, P06899 0.105
30 8EVJ EM 4.10 2023-11-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 138 CX3CR1 nucleosome bound PU.1 and C/EBPa Lian, T., Guan, R., Zhou, B.R., Bai, Y. 10.1038/s41594-023-01189-z 38267599 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 ScFv, Transcription factor PU.1 Transcription factors, Euchromatin-associated, Transcription-associated P17433 P68431, P62805, Q16778, Q16777 0.31
31 8BZ1 EM 3.80 2023-05-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 198 RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W) Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., Cramer, P. 10.1016/j.molcel.2023.04.011 37148879 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription initiation factor IIB, TATA-box-binding protein, General transcription factor IIF subunit 1, General transcription factor IIF subunit 2, Transcription initiation factor IIA subunit 1, Transcription initiation factor IIA subunit 2 Transcription factors, Transcription-associated, RNA polymerases, Euchromatin-associated A0A8D1DPV6, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, I3LJZ9, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A4X1TRS6, Q00403, P20226, P35269, P13984, P52655, P52657 P06897, P84233, P62799, P02281 0.244
32 6S01 EM 3.20 2019-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome Wang, H., Farnung, L., Dienemann, C., Cramer, P. 10.1038/s41594-019-0345-4 31819277 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2019 PC4 and SFRS1-interacting protein Histone_methylation_H3K36_reader, Histone PTM readers, Transcription factors, Transcription-associated O75475 P06897, P84233, P62799, P02281 0.529
33 7XZZ EM 4.07 2022-10-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 155 Cryo-EM structure of the nucleosome in complex with p53 Nishimura, M., Takizawa, Y., Nozawa, K., Kurumizaka, H. 10.1093/pnasnexus/pgac177 36714865 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Cellular tumor antigen p53 Transcription-associated, Transcription factors, Cell cycle, DNA repair P04637 P04908, P68431, P62805, P06899 0.192
34 9II7 EM 3.50 2025-06-11 hexamer 1 H3.3 canonical_H4 H2A.B canonical_H2B 601_modified 114 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B Akatsu, M., Hirano, R., Kujirai, T., Ogasawara, M., Ehara, H., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1038/s44318-025-00473-6 40447801 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, C4QY79, C4R009, C4R3Z5, C4QWA8, C4QZ45, C4R0E6, C4R370 P0C5Z0, P62805, P06899, P84243 0.285
35 9EGZ EM 2.90 2024-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 159 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27 Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_methylation_H3K36_writer, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267, Q9BYW2 A0A310TTQ1, P06897, P62799, P02281 0.261
36 8VFY EM 2.89 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 171 Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 1) Zhou, B.R., Feng, H., Huang, F., Zhu, I., Portillo-Ledesma, S., Shi, D., Zaret, K.S., Schlick, T., Landsman, D., Wang, Q., Bai, Y. 10.1016/j.molcel.2024.07.016 39121853 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Hepatocyte nuclear factor 3-alpha Transcription factors, Transcription-associated P55317 P04908, P68431, P62805, P06899 0.463
37 8UBL EM 2.80 2026-01-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 162 Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome (3D Flex map) Zhou, B.R., Bai, Y. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 scFv, Achaete-scute homolog 1, Transcription factor E2-alpha Heterochromatin-associated, Transcription factors, Transcription-associated Q02067, P15806 P04908, P68431, P62805, P06899 0.506
38 8BVW EM 4.00 2023-05-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 206 RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., Cramer, P. 10.1016/j.molcel.2023.04.011 37148879 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 General transcription and DNA repair factor IIH helicase subunit XPB, TFIIH basal transcription factor complex helicase XPD subunit, General transcription factor IIH subunit 1, General transcription factor IIH subunit 4, General transcription factor IIH subunit 2, General transcription factor IIH subunit 3, General transcription factor IIH subunit 5, CDK-activating kinase assembly factor MAT1, Cyclin-dependent kinase 7, Cyclin-H, DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription initiation factor IIB, TATA-box-binding protein, General transcription factor IIF subunit 1, General transcription factor IIF subunit 2, Transcription initiation factor IIA subunit 1, Transcription initiation factor IIA subunit 2, General transcription factor IIE subunit 1, Transcription initiation factor IIE subunit beta Transcription-associated, Cell cycle, Transcription factors, RNA polymerases, DNA repair, Euchromatin-associated P19447, P18074, P32780, Q92759, Q13888, Q13889, Q6ZYL4, P51948, P50613, P51946, A0A7M4DUC2, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A4X1TRS6, Q00403, P20226, P35269, P13984, P52655, P52657, P29083, P29084 P06897, P84233, P62799, P02281 0.234
39 7ZS9 EM 3.10 2022-11-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 209 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. 10.1038/s41594-022-00865-w 36411341 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta Transcription factors, RNA polymerases, Transcription-associated, DNA repair, Euchromatin-associated P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145 P06897, P84233, P62799, P02281 0.34
40 7XSZ EM 3.40 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 155 RNA polymerase II elongation complex transcribing a nucleosome (EC115) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.248
41 7UNC EM 3.00 2022-10-19 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 155 Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome Filipovski, M., Soffers, J.H.M., Vos, S.M., Farnung, L. 10.1126/science.abo3851 35709268 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RPOL4c domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, RPB8, RPB9, RPB10, RPB11, RNA polymerase II subunit K, Transcription elongation factor SPT6, Transcription elongation factor A protein 1, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, A0A4X1TVZ5, A0A481DF93, A0A8D1GCS3, A0A4X1VTX4, A0A4X1VEK9, A0A4X1VKG7, A0A4X1TRS6, Q7KZ85, P23193, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, O00267 Q6AZJ8, P84233, P62799, P02281 0.344
42 7ZSA EM 4.00 2022-11-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 209 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Wang, H., Schilbach, S., Ninov, M., Urlaub, H., Cramer, P. 10.1038/s41594-022-00865-w 36411341 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2022 General transcription and DNA repair factor IIH helicase subunit XPD, General transcription and DNA repair factor IIH subunit TFB1, General transcription and DNA repair factor IIH subunit TFB2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH subunit SSL1, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-box-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta Transcription factors, RNA polymerases, Transcription-associated, DNA repair, Euchromatin-associated P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145 P06897, P84233, P62799, P02281 0.342
43 7XTD EM 3.90 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 123 RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone chaperones, FACT, SPT4-SPT5 complex, DNA replication, DNA repair, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.221
44 9WMU EM 4.28 2025-12-24 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 171 Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Kujirai, T., Ehara, H., Ito, T., Henmi, M., Oya, E., Kobayashi, T., Sekine, S.I., Kurumizaka, H. 10.1126/sciadv.aed1952 41604494 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Histone-lysine N-methyltransferase, H3 lysine-36 specific, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4QY01, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.189
45 9WMS EM 3.40 2025-12-24 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 118 Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Kujirai, T., Ehara, H., Ito, T., Henmi, M., Oya, E., Kobayashi, T., Sekine, S.I., Kurumizaka, H. 10.1126/sciadv.aed1952 41604494 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Histone-lysine N-methyltransferase, H3 lysine-36 specific, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4QY01, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.227
46 9R2M EM 3.50 2025-07-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 143 p53 bound to nucleosome at position SHL+5.9 (non-crosslinked sample, composite map) Chakraborty, D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Cellular tumor antigen p53 Transcription-associated, Transcription factors, Cell cycle, DNA repair P04637 P04908, P68431, P62805, P06899 0.39
47 8PKI EM 2.58 2024-02-28 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601 137 Cryo-EM structure of NR5A2-nucleosome complex SHL+5.5 Kobayashi, W., Sappler, A.H., Bollschweiler, D., Kummecke, M., Basquin, J., Arslantas, E.N., Ruangroengkulrith, S., Hornberger, R., Duderstadt, K., Tachibana, K. 10.1038/s41594-024-01239-0 38409506 Mus musculus Mus musculus Mus musculus Mus musculus Xenopus laevis 2024 Nuclear receptor subfamily 5 group A member 2 Transcription factors, Transcription-associated O00482 P62806, P84244, Q6ZWY9, C0HKE3 0.572
48 8CBN EM 3.34 2023-12-27 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Histone_methylation_H3K36_reader, Histone PTM readers, Transcription factors, Transcription-associated O75475 P06897, P84233, P62799, P02281 0.392
49 8BYQ EM 4.10 2023-05-03 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 198 RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Abril-Garrido, J., Dienemann, C., Grabbe, F., Velychko, T., Lidschreiber, M., Wang, H., Cramer, P. 10.1016/j.molcel.2023.04.011 37148879 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 General transcription and DNA repair factor IIH helicase subunit XPB, TFIIH basal transcription factor complex helicase XPD subunit, General transcription factor IIH subunit 1, General transcription factor IIH subunit 4, General transcription factor IIH subunit 2, General transcription factor IIH subunit 3, General transcription factor IIH subunit 5, CDK-activating kinase assembly factor MAT1, Cyclin-dependent kinase 7, Cyclin-H, DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription initiation factor IIB, TATA-box-binding protein, General transcription factor IIF subunit 1, General transcription factor IIF subunit 2, Transcription initiation factor IIA subunit 1, Transcription initiation factor IIA subunit 2, General transcription factor IIE subunit 1, Transcription initiation factor IIE subunit beta Transcription-associated, Cell cycle, Transcription factors, RNA polymerases, DNA repair, Euchromatin-associated P19447, P18074, P32780, Q92759, Q13888, Q13889, Q6ZYL4, P51948, P50613, P51946, A0A7M4DUC2, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A4X1TRS6, Q00403, P20226, P35269, P13984, P52655, P52657, P29083, P29084 P06897, P84233, P62799, P02281 0.187
50 7XZX EM 4.53 2022-10-12 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 171 Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain Nishimura, M., Takizawa, Y., Nozawa, K., Kurumizaka, H. 10.1093/pnasnexus/pgac177 36714865 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 Cellular tumor antigen p53 Transcription-associated, Transcription factors, Cell cycle, DNA repair P04637 P04908, P68431, P62805, P06899 0.146
51 9RZE EM 8.53 2026-03-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 181 State 2 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to proximal upstream H3 Walshe, J.L., Ochmann, M., Neef, U., Dybkov, O., Dienemann, C., Oberthur, C., Zheenbekova, A., Urlaub, H., Cramer, P. 10.1038/s41467-025-65439-y 41162378 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription elongation factor SPT6, Histone-lysine N-methyltransferase SETD2, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WD repeat-containing protein 61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit SPT16 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K36_writer, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, FACT, DNA replication, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated, DNA repair A0A8D1DPV6, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A8D1KNW4, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A8D0JYF1, Q7KZ85, Q9BYW2, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, Q4R941, O00267, Q9Y5B9 O60814, Q71DI3, P04908, P62805 0.068
52 6T7B EM 5.10 2020-04-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 95 Structure of human Sox2 transcription factor in complex with a nucleosome Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P. 10.1038/s41586-020-2195-y 32350470 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Transcription factor SOX-2 Transcription factors, Transcription-associated P48431 O60814, Q71DI3, P04908, P62805 0.217
53 9RMC EM 4.20 2026-02-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 131 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 1 Vecchia, L., Weiss, J., Cavadini, S., Kempf, G., Kater, L., Pathare, G., Thoma, N.H. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Transcription activator BRG1, Actin-like protein 6A, Actin, cytoplasmic 1, N-terminally processed, AT-rich interactive domain-containing protein 1A, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, SWI/SNF complex subunit SMARCC2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1, Zinc finger protein ubi-d4, Green fluorescent protein,POU domain, class 5, transcription factor 1, Transcription factor SOX-2 Cell cycle, Transcription factors, Transcription-associated, Chromatin remodelers, SWI/SNF P51532, O96019, P60709, O14497, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q92785, P42212, P48431 P04908, P68431, P62805, P06899 0.242
54 9J0P EM 3.30 2025-02-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 191 Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc) Naganuma, M., Kujirai, T., Ehara, H., Uejima, T., Ito, T., Goto, M., Aoki, M., Henmi, M., Miyamoto-Kohno, S., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/sciadv.adu0577 40043114 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RPB12, Negative elongation factor A, Negative elongation factor B, Negative elongation factor C/D, Negative elongation factor E, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Euchromatin-associated A0A8D1DPV6, A0A0B8RVL1, I3LCH3, A0A481BYI6, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A8W4F9W9, F1RKE4, A0A4X1TRS6, Q9H3P2, Q8WX92, Q8IXH7, P18615, P63272, O00267 P04908, P62805, P06899, P84243 0.311
55 8SPU EM 2.80 2023-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 149 Structure of ESRRB nucleosome bound OCT4 at site c Guan, R., Lian, T., Zhou, B.R., Wheeler, D., Bai, Y. 10.1016/j.molcel.2023.05.030 37327775 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 ScFv, Maltodextrin-binding protein,POU domain, class 5, transcription factor 1 Transcription factors, Euchromatin-associated, Transcription-associated Q01860 P68431, P62805, Q16778, Q16777 0.496
56 8OTS EM 3.30 2023-05-24 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 127 OCT4 and MYC-MAX co-bound to a nucleosome Michael, A.K., Stoos, L., Crosby, P., Eggers, N., Nie, X.Y., Makasheva, K., Minnich, M., Healy, K.L., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, R.S., Andersch, F., Fribourgh, J.L., Schubeler, D., Zuber, J., Liu, A.C., Becker, P.B., Fierz, B., Partch, C.L., Menet, J.S., Thoma, N.H. 10.1038/s41586-023-06282-3 37407816 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Green fluorescent protein,POU domain, class 5, transcription factor 1, Myc proto-oncogene protein, Protein max Transcription factors, Transcription-associated P42212, P01106, P61244 P04908, P68431, P62805, P06899 0.404
57 8CBQ EM 4.00 2023-09-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 150 structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Histone_methylation_H3K36_reader, Histone PTM readers, Transcription factors, Transcription-associated O75475 P06897, P84233, P62799, P02281 0.304
58 6T7C EM 4.00 2020-04-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 95 Structure of two copies of human Sox11 transcription factor in complex with a nucleosome Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P. 10.1038/s41586-020-2195-y 32350470 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Transcription factor SOX-11 Transcription factors, Transcription-associated P35716 O60814, Q71DI3, P04908, P62805 0.355
59 9WMW EM 3.62 2025-12-24 hexamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 75 Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Kujirai, T., Ehara, H., Ito, T., Henmi, M., Oya, E., Kobayashi, T., Sekine, S.I., Kurumizaka, H. 10.1126/sciadv.aed1952 41604494 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Histone-lysine N-methyltransferase, H3 lysine-36 specific, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, FACT, SPT4-SPT5 complex, DNA replication, DNA repair, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4QY01, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.229
60 7XSX EM 3.80 2022-09-07 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 108 RNA polymerase II elongation complex transcribing a nucleosome (EC49) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone chaperones, FACT, SPT4-SPT5 complex, DNA replication, DNA repair, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.227
61 9RN1 EM 5.90 2026-02-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 134 Structure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47 bound to ATPase lobe 2 Na, N.A. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Transcription activator BRG1, Actin-like protein 6A, Actin, cytoplasmic 1, N-terminally processed, AT-rich interactive domain-containing protein 1A, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, SWI/SNF complex subunit SMARCC2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1, Zinc finger protein ubi-d4, Green fluorescent protein,POU domain, class 5, transcription factor 1, Transcription factor SOX-2 Cell cycle, Transcription factors, Transcription-associated, Chromatin remodelers, SWI/SNF P51532, O96019, P60709, O14497, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q92785, P42212, P48431 P04908, P68431, P62805, P06899 0.227
62 9IGJ EM 3.80 2026-03-04 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 125 structure of two human ELF2 transcription factors in complex with a nucleosome Xiao, T., Crowe-McAuliffe, C., Ochmann, M., Du, Y., Hou, T., Chen, Y., Zhu, F., Seyednasrollah, F., Osmala, M., Vanharanta, S., Morgunova, E., Cramer, P., Rogerson, C., Dienemann, C., Taipale, J. 0 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2026 ETS-related transcription factor Elf-2 Transcription factors, Transcription-associated Q15723 P06897, P02281, P62799, None 0.329
63 8VG1 EM 2.48 2024-08-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 171 Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome Zhou, B.R., Feng, H., Huang, F., Zhu, I., Portillo-Ledesma, S., Shi, D., Zaret, K.S., Schlick, T., Landsman, D., Wang, Q., Bai, Y. 10.1016/j.molcel.2024.07.016 39121853 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2024 Hepatocyte nuclear factor 3-alpha, Maltose/maltodextrin-binding periplasmic protein,Transcription factor GATA-4 Transcription factors, Transcription-associated P55317, P0AEX9 P04908, P68431, P62805, P06899 0.541
64 9RL4 EM 3.50 2026-02-11 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 142 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6 Lastname, F.M. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 Transcription activator BRG1, Actin-like protein 6A, Actin, cytoplasmic 1, N-terminally processed, AT-rich interactive domain-containing protein 1A, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, SWI/SNF complex subunit SMARCC2, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1, Zinc finger protein ubi-d4, Green fluorescent protein,POU domain, class 5, transcription factor 1, Transcription factor SOX-2 Cell cycle, Transcription factors, Transcription-associated, Chromatin remodelers, SWI/SNF P51532, O96019, P60709, O14497, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q92785, P42212, P48431 P04908, P68431, P62805, P06899 0.386
65 7NKY EM 3.20 2021-07-07 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 148 RNA Polymerase II-Spt4/5-nucleosome-FACT structure Farnung, L., Ochmann, M., Engeholm, M., Cramer, P. 10.1038/s41594-021-00578-6 33846633 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, FACT complex subunit POB3, FACT complex subunit SPT16, Chromatin elongation factor SPT4, Transcription elongation factor SPT5 Transcription-associated, RNA polymerases, Transcription factors, Centromere-associated, Histone chaperones, Heterochromatin-associated, FACT, SPT4-SPT5 complex, DNA replication, DNA repair, Euchromatin-associated P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, Q04636, P32558, P32914, P27692 P06897, P84233, P62799, P02281 0.358
66 7OH9 EM 3.00 2021-07-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 145 Nucleosome with TBP and TFIIA bound at SHL -6 Wang, H., Xiong, L., Cramer, P. 10.1073/pnas.2108859118 34301908 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2021 TATA-binding protein, Transcription initiation factor IIA large subunit, Transcription initiation factor IIA subunit 2 Transcription factors, Transcription-associated P13393, P32773, P32774 P06897, P84233, P62799, P02281 0.49
67 9J0O EM 3.30 2025-02-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 191 Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC1-nuc) Naganuma, M., Kujirai, T., Ehara, H., Uejima, T., Ito, T., Goto, M., Aoki, M., Henmi, M., Miyamoto-Kohno, S., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/sciadv.adu0577 40043114 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RPB12, Negative elongation factor A, Negative elongation factor B, Negative elongation factor C/D, Negative elongation factor E, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Euchromatin-associated A0A8D1DPV6, A0A0B8RVL1, I3LCH3, A0A481BYI6, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A8W4F9W9, F1RKE4, A0A4X1TRS6, Q9H3P2, Q8WX92, Q8IXH7, P18615, P63272, O00267 P04908, P62805, P06899, P84243 0.313
68 8SPS EM 3.00 2023-06-28 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 147 High resolution structure of ESRRB nucleosome bound OCT4 at site a and site b Guan, R., Lian, T., Zhou, B.R., Wheeler, D., Bai, Y. 10.1016/j.molcel.2023.05.030 37327775 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 ScFv, Maltodextrin-binding protein,POU domain, class 5, transcription factor 1 Transcription factors, Euchromatin-associated, Transcription-associated Q01860 P68431, P62805, Q16778, Q16777 0.434
69 8PC5 EM 3.02 2023-08-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Histone_methylation_H3K36_reader, Histone PTM readers, Transcription factors, Transcription-associated O75475 P06897, P84233, P62799, P02281 0.521
70 8EVI EM 2.64 2023-11-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 143 CX3CR1 nucleosome and PU.1 complex containing disulfide bond mutations Lian, T., Guan, R., Zhou, B.R., Bai, Y. 10.1038/s41594-023-01189-z 38267599 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Single-chain variable fragment, Transcription factor PU.1 Transcription factors, Euchromatin-associated, Transcription-associated P17433 P68431, P62805, Q16778, Q16777 0.559
71 6IR9 EM 3.80 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 128 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Spt5 Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.264
72 8PEO EM 2.69 2023-08-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Histone_methylation_H3K36_reader, Histone PTM readers, Transcription factors, Transcription-associated O75475 P06897, P84233, P62799, P02281 0.548
73 6T90 EM 3.05 2020-05-06 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 141 OCT4-SOX2-bound nucleosome - SHL-6 Michael, A.K., Grand, R.S., Isbel, L., Cavadini, S., Kozicka, Z., Kempf, G., Bunker, R.D., Schenk, A.D., Graff-Meyer, A., Pathare, G.R., Weiss, J., Matsumoto, S., Burger, L., Schubeler, D., Thoma, N.H. 10.1126/science.abb0074 32327602 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Green fluorescent protein,POU domain, class 5, transcription factor 1, Transcription factor SOX-2 Transcription factors, Transcription-associated P42212, P48431 P04908, P68431, P62805, P06899 0.451
74 7WBX EM 4.00 2023-07-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 150 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.298
75 9R04 EM 4.20 2025-07-02 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 142 p53 bound to the nucleosome at position SHL-5.7 (crosslinked sample) Chakraborty, D. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 Cellular tumor antigen p53 Transcription-associated, Transcription factors, Cell cycle, DNA repair P04637 P04908, P68431, P62805, P06899 0.232
76 9EGY EM 2.90 2024-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 160 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-nucleosome, bp +27 Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267 A0A310TTQ1, P06897, P62799, P02281 0.256
77 9EH0 EM 3.60 2024-12-18 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 181 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 30 bp upstream Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_methylation_H3K36_writer, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267, Q9BYW2 A0A310TTQ1, P06897, P62799, P02281 0.24
78 8UBK EM 2.60 2026-01-21 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 162 Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome Zhou, B.R., Bai, Y. 0 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2026 scFv, Achaete-scute homolog 1, Transcription factor E2-alpha Heterochromatin-associated, Transcription factors, Transcription-associated Q02067, P15806 P04908, P68431, P62805, P06899 0.514
79 8G88 EM 2.30 2023-03-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 168 Human Oct4 bound to nucleosome with human nMatn1 sequence Sinha, K.K., Bilokapic, S., Du, Y., Malik, D., Halic, M. 10.1038/s41586-023-06112-6 37225990 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 POU domain, class 5, transcription factor 1 Transcription factors, Euchromatin-associated, Transcription-associated Q01860 Q6AZJ8, P84233, P62799, P02281 0.199
80 7XTI EM 3.90 2022-10-12 hexamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 85 RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone chaperones, FACT, SPT4-SPT5 complex, DNA replication, DNA repair, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4QYQ8, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.223
81 6T7D EM 4.40 2020-04-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 117 Structure of human Sox11 transcription factor in complex with a nucleosome Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P. 10.1038/s41586-020-2195-y 32350470 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Transcription factor SOX-11 Transcription factors, Transcription-associated P35716 O60814, Q71DI3, P04908, P62805 0.323
82 6T7A EM 3.70 2020-04-29 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B DNA-1 95 Structure of human Sox11 transcription factor in complex with a nucleosome Dodonova, S.O., Zhu, F., Dienemann, C., Taipale, J., Cramer, P. 10.1038/s41586-020-2195-y 32350470 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2020 Transcription factor SOX-11 Transcription factors, Transcription-associated P35716 O60814, Q71DI3, P04908, P62805 0.37
83 6J4Z EM 4.10 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 128 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor SPT4, Spt5 Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.244
84 6J4Y EM 4.30 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 127 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.235
85 9J0N EM 3.40 2025-02-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 167 Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc) Naganuma, M., Kujirai, T., Ehara, H., Uejima, T., Ito, T., Goto, M., Aoki, M., Henmi, M., Miyamoto-Kohno, S., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/sciadv.adu0577 40043114 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit F, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RPB12, Transcription elongation factor A protein 1, Negative elongation factor A, Negative elongation factor B, Negative elongation factor C/D, Negative elongation factor E, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Euchromatin-associated A0A8D1DPV6, A0A0B8RVL1, I3LCH3, A0A481BYI6, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A8W4F9W9, F1RKE4, A0A4X1TRS6, P23193, Q9H3P2, Q8WX92, Q8IXH7, P18615, P63272, O00267 P04908, P62805, P06899, P84243 0.316
86 9S3G EM 6.40 2025-11-12 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 67 State 1 MAP3 RNA Pol II activated elongation complex with SETD2 and upstream hexasome Walshe, J.L., Ochmann, M., Neef, U., Dybkov, O., Dienemann, C., Oberthur, C., Zheenbekova, A., Urlaub, H., Cramer, P. 10.1038/s41467-025-65439-y 41162378 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, Transcription elongation factor SPT6, Histone-lysine N-methyltransferase SETD2, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WD repeat-containing protein 61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit SPT16, FACT complex subunit SSRP1 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K36_writer, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, FACT, DNA replication, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated, DNA repair A0A8D1DPV6, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A8D1KNW4, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A8D0JYF1, Q7KZ85, Q9BYW2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, Q4R941, O00267, Q9Y5B9, Q08945 O60814, Q71DI3, P04908, P62805 0.187
87 8G8G EM 3.20 2023-03-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 174 Interaction of H3 tail in LIN28B nucleosome with Oct4 Sinha, K.K., Bilokapic, S., Du, Y., Malik, D., Halic, M. 10.1038/s41586-023-06112-6 37225990 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 POU domain, class 5, transcription factor 1 Transcription factors, Euchromatin-associated, Transcription-associated Q01860 Q6AZJ8, P84233, P62799, P02281 0.218
88 8PEP EM 3.33 2023-08-16 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 147 H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Koutna, E., Lux, V., Kouba, T., Skerlova, J., Novacek, J., Srb, P., Hexnerova, R., Svachova, H., Kukacka, Z., Novak, P., Fabry, M., Poepsel, S., Veverka, V. 10.1093/nar/gkad674 37615563 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 PC4 and SFRS1-interacting protein Histone_methylation_H3K36_reader, Histone PTM readers, Transcription factors, Transcription-associated O75475 P06897, P84233, P62799, P02281 0.399
89 8G8B EM 4.30 2023-03-22 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 168 Nucleosome with human nMatn1 sequence in complex with Human Oct4 Sinha, K.K., Bilokapic, S., Du, Y., Malik, D., Halic, M. 10.1038/s41586-023-06112-6 37225990 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2023 POU domain, class 5, transcription factor 1 Transcription factors, Euchromatin-associated, Transcription-associated Q01860 Q6AZJ8, P84233, P62799, P02281 0.233
90 8EVH EM 2.85 2023-11-01 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 141 CX3CR1 nucleosome and wild type PU.1 complex Lian, T., Guan, R., Zhou, B.R., Bai, Y. 10.1038/s41594-023-01189-z 38267599 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 Single-chain variable fragment, Transcription factor PU.1 Transcription factors, Euchromatin-associated, Transcription-associated P17433 P68431, P62805, Q16778, Q16777 0.509
91 8A3Y EM 3.30 2024-07-31 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601_modified 138 Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex Farnung, L., Ochmann, M., Garg, G., Vos, S.M., Cramer, P. 10.1016/j.molcel.2022.06.027 35858621 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase II subunit D, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, RNA polymerase II subunit K, SPT6, RNA polymerase-associated protein CTR9 homolog,RNA polymerase-associated protein LEO1, RNA polymerase-associated protein RTF1 homolog, RNA polymerase II-associated factor 1 homolog, WD repeat-containing protein 61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated A0A7M4DUC2, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, A0A8D0JYF1, Q7KZ85, Q6PD62, Q92541, Q8N7H5, Q9GZS3, Q6P1J9, Q4R941, O00267 Q6AZJ8, P84233, A0A8J1LZU9, P62799 0.231
92 7XT7 EM 4.20 2022-10-12 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 126 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.abp9466 35981082 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2022 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, FACT complex subunit, FACT complex subunit POB3, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone chaperones, FACT, SPT4-SPT5 complex, DNA replication, DNA repair, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, F2QPX0, F2QNN8, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.207
93 7WBW EM 7.10 2023-07-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 154 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.137
94 7WBV EM 4.10 2023-07-05 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 159 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Osumi, K., Kujirai, T., Ehara, H., Ogasawara, M., Kinoshita, C., Saotome, M., Kagawa, W., Sekine, S.I., Takizawa, Y., Kurumizaka, H. 10.1016/j.jmb.2023.168130 37120012 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2023 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5 Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.267
95 9WMT EM 3.59 2025-12-24 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 121 Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Kujirai, T., Ehara, H., Ito, T., Henmi, M., Oya, E., Kobayashi, T., Sekine, S.I., Kurumizaka, H. 10.1126/sciadv.aed1952 41604494 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2025 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, DNA-directed RNA polymerases I, II, and III subunit RPABC1, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Transcription elongation factor Spt6, Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II, Component of the Paf1p complex, RNAPII-associated chromatin remodeling Paf1 complex subunit, Histone-lysine N-methyltransferase, H3 lysine-36 specific, Leo1, RNAP II-associated protein, Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, C4R7H2, C4R7L8, C4R6B2, F2QQ42, C4QY01, C4R3K1, C4R997, C4R1E6 P04908, P62805, P06899, P84243 0.225
96 9EH2 EM 3.10 2024-12-18 hexamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 65 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream Markert, J.W., Soffers, J.H., Farnung, L. 10.1126/science.adn6319 39666822 Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis Xenopus laevis 2024 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase II subunit RPB3, RNA polymerase Rpb4/RPC9 core domain-containing protein, DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, RNA polymerase II subunit J, RNA polymerase II subunit K, Transcription elongation factor SPT6, Protein IWS1 homolog, RNA polymerase-associated protein CTR9 homolog, RNA polymerase-associated protein RTF1 homolog, Transcription elongation factor A protein 1, RNA polymerase-associated protein LEO1, RNA polymerase II-associated factor 1 homolog, WDR61, Parafibromin, Transcription elongation factor SPT4, Transcription elongation factor SPT5, Histone-lysine N-methyltransferase SETD2, FACT complex subunit SPT16, FACT complex subunit SSRP1 Transcription factors, Transcription-associated, RNA polymerases, Histone PTM writers, Histone chaperones, Histone_methylation_H3K4_writer, PAF1C, Cell cycle, Histone_methylation_H3K36_writer, FACT, DNA replication, Histone_ubiquitination_H2BK120_writer, Euchromatin-associated, DNA repair A0A7M4DUC2, A0A0B8RVL1, I3LCH3, A0A8D0KES4, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A8D1AQR7, P60899, A0A8W4F9W9, A0A8D0TE17, A0A4X1TRS6, Q7KZ85, Q96ST2, Q6PD62, Q92541, P23193, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267, Q9BYW2, Q9Y5B9, Q08945 A0A310TTQ1, P06897, P62799, P02281 0.252
97 8CEO EM 3.60 2023-03-08 octamer 1 canonical_H3 canonical_H4 canonical_H2A canonical_H2B 601 209 Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Schilbach, S., Wang, H., Dienemann, C., Cramer, P. 10.1073/pnas.2220542120 37014863 Xenopus laevis Xenopus laevis Xenopus laevis Saccharomyces cerevisiae Xenopus laevis 2023 General transcription and DNA repair factor IIH helicase subunit XPD, TFB1 isoform 1, RNA polymerase II transcription factor B subunit 2, RNA polymerase II transcription factor B subunit 3, General transcription and DNA repair factor IIH subunit TFB4, General transcription and DNA repair factor IIH subunit TFB5, General transcription and DNA repair factor IIH, General transcription and DNA repair factor IIH helicase subunit XPB, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerases I, II, and III subunit RPABC4, Transcription initiation factor IIB, TATA-binding protein, Transcription initiation factor IIF subunit alpha, Transcription initiation factor IIF subunit beta, TOA1 isoform 1, Transcription initiation factor IIA subunit 2, Transcription initiation factor IIE subunit alpha, Transcription initiation factor IIE subunit beta, Mediator of RNA polymerase II transcription subunit 6, Mediator of RNA polymerase II transcription subunit 8, Mediator of RNA polymerase II transcription subunit 11, Mediator of RNA polymerase II transcription subunit 17, Mediator of RNA polymerase II transcription subunit 18, Mediator of RNA polymerase II transcription subunit 20, Mediator of RNA polymerase II transcription subunit 22, Mediator of RNA polymerase II transcription subunit 4, Mediator of RNA polymerase II transcription subunit 7, Mediator of RNA polymerase II transcription subunit 9, Mediator of RNA polymerase II transcription subunit 10, Mediator of RNA polymerase II transcription subunit 14, Mediator of RNA polymerase II transcription subunit 19, Mediator of RNA polymerase II transcription subunit 21, Mediator of RNA polymerase II transcription subunit 31, Mediator of RNA polymerase II transcription subunit 1 Transcription factors, RNA polymerases, Transcription-associated, Mediator, DNA repair, Euchromatin-associated P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145, P38782, P38304, Q99278, P32569, P32585, P34162, P32570, Q12343, Q08278, P33308, Q06213, P19263, P25046, P47822, P38633, Q12321 P06897, P84233, P62799, P02281 0.222
98 6J51 EM 4.20 2019-02-20 octamer 1 H3.3 canonical_H4 canonical_H2A canonical_H2B 601_modified 127 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I. 10.1126/science.aav8912 30733384 Homo sapiens Homo sapiens Homo sapiens Homo sapiens Xenopus laevis 2019 DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, RNA polymerase II third largest subunit B44, part of central core, RNA polymerase II subunit B32, RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III, RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III, RNA polymerase II subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC3, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, RNA polymerase subunit ABC10-alpha, Transcription elongation factor 1 homolog, Transcription elongation factor SPT4, Protein that forms a complex with Spt4p Transcription factors, Transcription-associated, RNA polymerases, SPT4-SPT5 complex, Euchromatin-associated C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370 P04908, P62805, P06899, P84243 0.23