New structures and tools
We are pleased to announce major updates to our nucleosome database, which now encompasses a comprehensive collection of 644 nucleosome structures. This expansion is part of our ongoing commitment to update the database annualy.
In addition to the expansion, we have integrated new features to enhance the usability and analytical capabilities of our database. For our cryoEM data, we have added backlinks to the Electron Microscopy Data Bank (EMDB). Furthermore, we added Q-score visualization, an essential tool for assessing the quality of cryoEM structures. This enhancement will enable researchers to evaluate the precision of individual nucleosome models more effectively.
We have also calculated local resolution maps for all structures with available halfmaps, offering detailed insights into the variable resolution within each structure.
You can also search by Uniprot ID to find interacting proteins or histones.
We invite researchers and scientists to explore the nucleosome database.
Nucleosome structures diversity
We have previously described the diversity of nucleosome structures, including DNA sequences, histone variants, taxa, and non-histone interactors, published in the first 25 years years following the initial release (as of September 2022). Now, we highlight some new and interesting structures published in 2023-2024.
Revealing a plant-specific variant
Despite the large number of histone variants presented in nucleosome structures, it was only last year that the first nucleosome with a plant-specific variant (H2A.W) was published [ 7UX9 ] . However, the unique SPKK motif at the C-terminal tail of histone H2A.W was not resolved in this structure.
Expanding Taxonomic Diversity
The diversity of histone taxa was further expanded by a nucleosome from the kinetoplastid parasite Trypanosoma brucei [ 8COM ] .
Beyond Histones
New structures with non-histone interactors were released in 2023-2024, including histone PTM writers and erasers (such as histone deacetylases and histone ubiquitination enzymes), the histone chaperone CAF-1, and a structure with a subunit of the telomere support Shelterin complex.
  • histone deacetylases
  • By the end of 2022, only one nucleosome structure with the yeast histone lysine deacetylase enzyme was released [ 6Z6P ] , containing HDAC class II Hda1-like proteins). In 2023-2024, the repertoire of nucleosome structures was enriched with representatives of other HDAC classes: human sirtuin 6 (HDAC class III Sir2-like proteins) [ 8OF4 8F86 8G57 ] , and the yeast Rpd3S complex (class I Rpd3-like proteins) [ 8KD2 8KD4 8KD5 8KD6 8KD7 8TOF 8HXY 8JHO 8HY0 ] . Structures with HDAC11, the sole representative of HDAC class IV, are eagerly awaited.
  • histone ubiquitination enzymes
  • Structures with new enzymes involved in H2B monoubiquitination were also published in 2023-2024. These structures include the Bre1 complex, which monoubiquitinates H2BK120/123 to regulate transcription elongation and DNA repair [ 8T3Y 8T3T 8IEG 8T3W ] , and the RNF168 complex, which produces and reads monoubiquitin at H2AK13 and H2AK15 during the DNA damage response a 21 structures.
  • histone chaperone CAF-1 in complexes with atypical right-handed ditetrasome
  • The set of complexes with histone chaperones included only multifunctional complex FACT and SPT6 (involved in transcription elongation). Last year, a nucleosome (more precisely right-handed di-tetrasome) with the human histone chaperone CAF-1 was released [ 8J6T 7Y61 7Y60 8J6S ] . CAF-1 promotes de novo nucleosome assembly during DNA replication. It binds newly synthesized H3.1-H4 histones and facilitates their deposition at the replication fork during the S phase.
  • structure with subunit of Shelterin complex which support telomeres
  • In addition to the telomeric nucleosome structures (obtained by the groups of Daniela Rhodes and Lars Nordenskiöld in 2020 and 2022), the first structure of telomeric nucleosome in complex with a Shelterin subunit was published in 2023 [ 8OX1 ] . Shelterin maintains genome stability by protecting chromosome ends from various DNA damage response and repair pathways.
Limitations and omissions
We acknowledge some known omissions in our database. Currently, some nucleosome intermediates, such as "disomes," are not included [ 8XBW ] . Nucleosome structures containig viral histone duplets are also omitted [ 7LV8 7LV9 7N8N ] , as well as archaeal [ 5T5K ] . Additionally, there exists a list of structures that are too large for our current analysis pipeline. [ 6KW4 6PWV 8GXQ 8GXS 8JNF 8OFF 8XBU 8XGC 7YI4 7YI5 8KD3 8RBX 8Q36 8Q3E 8Q3M 8Q3X 8QKT 8OW1 ] We are working on addressing these limitations to ensure our database remains complete.