5B40

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.33 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E
139Homo sapiensMutation(s): 1 
Gene Names: HIST2H3AHIST2H3CH3F2H3FMHIST2H3DH3C15H3C14H3C13
Find proteins for Q71DI3 (Homo sapiens)
Go to UniProtKB:  Q71DI3
NIH Common Fund Data Resources
PHAROS  Q71DI3

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
106Homo sapiensMutation(s): 1 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS  P62805

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1-B/E
C, G
133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFAH2AC4H2AC8
Find proteins for P04908 (Homo sapiens)
Go to UniProtKB:  P04908
NIH Common Fund Data Resources
PHAROS  P04908

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-J
D, H
129Homo sapiensMutation(s): 1 
Gene Names: HIST1H2BJH2BFRH2BC11
Find proteins for P06899 (Homo sapiens)
Go to UniProtKB:  P06899
NIH Common Fund Data Resources
PHAROS  P06899

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsLengthOrganism
DNA (146-MER)I, J146Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.33 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.419α = 90
b = 100.419β = 90
c = 186.025γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



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
  • Version 1.1: 2020-02-26
    Changes: Data collection, Derived calculations