6UPH

Structure of a Yeast Centromeric Nucleosome at 2.7 Angstrom resolution

Exp. Method EM
Resolution, Å 2.7
Release Date 2019-11-06
Update Date 2022-11-16
Authors Migl, D., Kschonsak, M., Arthur, C.P., Khin, Y., Harrison, S.C., Ciferri, C., Dimitrova, Y.N.
Publication PMID: 32004465
doi 10.1016/j.str.2019.12.002
RCSB PDB 6UPH
EMDB EMD-20839
Q-score 0.623
Core histones in Nucleosome-like particles:
Side Chain HistoneDB Variant Taxa UID
H3 Proximal A cenH3 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) P36012
Distal E cenH3 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) P36012
H4 Proximal B canonical H4 Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) Q6CMU6
Distal F canonical H4 Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) Q6CMU6
H2A Proximal C H2A.X Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) Q6CK59
Distal G H2A.X Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) Q6CK59
H2B Proximal D canonical H2B Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) Q6CK60
Distal H canonical H2B Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) Q6CK60
DNA:
Chain Variant Length
I 601 119
J 601 119

H3

H4

H2A

H2B

DNA

Other


Chain Bfactor Q-score Local Resolution

Aligned nucleosome coordinates

Nucleosome reference frame definition

DNA relative twist and local base step parameters

Sequence on X-axis is numbered relative to the dyad base pair.

Atomic contacts between nucleosomal entities.


Hover the mouse cursor on the barplot to show contact information. Oncogenic mutations of non-histone proteins in contact are highlighted.