The nucleosome structure containing H2B-K120 and H4-K31 monoubiquitinations

Experimental Data Snapshot

  • Resolution: 3.33 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history


Monoubiquitination of histones H2B and H4 changes the nucleosome stability without affecting the nucleosome structure

Machida, S.Sekine, S.Nishiyama, Y.Horikoshi, N.Kurumizaka, H.

To be published.


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E
139Homo sapiensMutation(s): 1 
Gene Names: HIST2H3A, HIST2H3C, HIST2H3D (H3F2, H3FM)
Find proteins for Q71DI3 (Homo sapiens)
Go to Gene View: HIST2H3A HIST2H3C HIST2H3D
Go to UniProtKB:  Q71DI3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
106Homo sapiensMutation(s): 1 
Gene Names: H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16 (H4/A, H4FA, HIST1H4A, H4/I, H4FI, HIST1H4B, H4/G, H4FG, HIST1H4C, H4/B, H4FB, HIST1H4D, H4/J, H4FJ, HIST1H4E, H4/C, H4FC, HIST1H4F, H4/H, H4FH, HIST1H4H, H4/M, H4FM, HIST1H4I, H4/E, H4FE, HIST1H4J, H4/D, H4FD, HIST1H4K, H4/K, H4FK, HIST1H4L, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4/O, H4FO, HIST2H4B, HIST4H4)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1-B/E
C, G
133Homo sapiensMutation(s): 0 
Gene Names: H2AC4, H2AC8 (H2AFM, HIST1H2AB, H2AFA, HIST1H2AE)
Find proteins for P04908 (Homo sapiens)
Go to UniProtKB:  P04908
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-J
D, H
129Homo sapiensMutation(s): 1 
Gene Names: H2BC11 (H2BFR, HIST1H2BJ)
Find proteins for P06899 (Homo sapiens)
Go to UniProtKB:  P06899
Entity ID: 5
DNA (146-MER)I,J146Homo sapiens
Experimental Data & Validation

Experimental Data

  • Resolution: 3.33 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.201 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 100.419α = 90.00
b = 100.419β = 90.00
c = 186.025γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
MEXT KAKENHIJapan25116002
JSPS KAKENHIJapan25250023
JSPS KAKENHIJapan26890023

Revision History 

  • Version 1.0: 2016-06-22
    Type: Initial release