5XM1

The mouse nucleosome structure containing H2A, H2B type3-A, H3mm7, and H4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The mouse nucleosome structure containing H2A, H2B type3-A, H3mm7, and H4

Taguchi, H.Horikoshi, N.Kurumizaka, H.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3mm7
A, E
139Mus musculusMutation(s): 0 
Gene Names: H3f3a, H3f3b (H3.3a, H3.3b)
Find proteins for P84244 (Mus musculus)
Go to UniProtKB:  P84244
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
106Mus musculusMutation(s): 0 
Gene Names: Hist1h4a, Hist1h4b, Hist1h4c, Hist1h4d, Hist1h4f, Hist1h4h, Hist1h4i, Hist1h4j, Hist1h4k, Hist1h4m, Hist2h4a, Hist4h4 (H4-53, H4-12, Hist2h4)
Find proteins for P62806 (Mus musculus)
Go to UniProtKB:  P62806
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1-B
C, G
133Mus musculusMutation(s): 0 
Gene Names: Hist1h2ab
Find proteins for C0HKE1 (Mus musculus)
Go to UniProtKB:  C0HKE1
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 3-A
D, H
129Mus musculusMutation(s): 0 
Gene Names: Hist3h2ba
Find proteins for Q9D2U9 (Mus musculus)
Go to UniProtKB:  Q9D2U9
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (146-MER)I,J146Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 105.550α = 90.00
b = 109.380β = 90.00
c = 176.209γ = 90.00
Software Package:
Software NamePurpose
HKLdata scaling
PHENIXrefinement
PHASERphasing
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan--
Ministry of Education, Culture, Sports, Science and TechnologyJapan25116002
the Japan Agency for Medical Research and DevelopmentJapan--

Revision History 

  • Version 1.0: 2018-03-07
    Type: Initial release