Human nucleosome containing CpG unmethylated DNA

Experimental Data Snapshot

  • Resolution: 3 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history


Crystal structure of human nucleosome core particle containing enzymatically introduced CpG methylation

Fujii, Y.Wakamori, M.Umehara, T.Yokoyama, S.

(2016) Febs Open Bio 6: 498-514


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 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): 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: 3 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 106.499α = 90.00
b = 109.047β = 90.00
c = 177.016γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and developmentJapanthe Platform Project for Supporting in Drug Discov
Japan Science and Technology AgencyJapanPRESTO program
Ministry of Education, Culture, Sports, Science and TechnologyJapanTargeted Proteins Research Program (TPRP)
Japan Society for the Promotion of Science LondonJapanC24613007
Takeda Science FoundationJapan--

Revision History 

  • Version 1.0: 2016-06-15
    Type: Initial release