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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2AE139Homo sapiensMutation(s): 1 
Gene Names: HIST2H3AHIST2H3CH3F2H3FMHIST2H3DH3C15H3C14H3C13
Find proteins for Q71DI3 (Homo sapiens)
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Go to UniProtKB:  Q71DI3
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PHAROS  Q71DI3
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4BF106Homo sapiensMutation(s): 1 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
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PHAROS  P62805
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/ECG133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFAH2AC4H2AC8
Find proteins for P04908 (Homo sapiens)
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Go to UniProtKB:  P04908
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PHAROS  P04908
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-JDH129Homo sapiensMutation(s): 1 
Gene Names: HIST1H2BJH2BFRH2BC11
Find proteins for P06899 (Homo sapiens)
Explore P06899 
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PHAROS  P06899
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Entity ID: 5
MoleculeChainsLengthOrganismImage
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