Crystal structure of the human nucleosome containing H2A.Z.1 S42R

Experimental Data Snapshot

  • Resolution: 2.17 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history


Stability of the nucleosome containing H2A.Z regulates transcription status in cells

Horikoshi, N.Kusakabe, M.Narimiya, T.Sato, K.Mizukami, Y.Takahashi, D.Kimura, H.Harata, M.Kurumizaka, H.

To be published.


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1
A, E
139Homo sapiensMutation(s): 0 
Gene Names: H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12 (H3FA, HIST1H3A, H3FL, HIST1H3B, H3FC HIST1H3C, H3FB, HIST1H3D, H3FD, HIST1H3E, H3FI, HIST1H3F, H3FH, HIST1H3G, H3FK, HIST1H3H, H3FF, HIST1H3I, H3FJ, HIST1H3J)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
106Homo sapiensMutation(s): 0 
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.Z
C, G
131Homo sapiensMutation(s): 1 
Gene Names: H2AZ1 (H2AFZ, H2AZ)
Find proteins for P0C0S5 (Homo sapiens)
Go to UniProtKB:  P0C0S5
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-J
D, H
129Homo sapiensMutation(s): 0 
Gene Names: H2BC11 (H2BFR, HIST1H2BJ)
Find proteins for P06899 (Homo sapiens)
Go to UniProtKB:  P06899
Entity ID: 5
DNA (146-MER)I,J146Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on MN

Download SDF File 
Download CCD File 
E, I, J
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Resolution: 2.17 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 98.955α = 90.00
b = 108.170β = 90.00
c = 169.812γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
BSSdata collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP25116002

Revision History 

  • Version 1.0: 2020-03-25
    Type: Initial release