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 H3.2A, E139Homo sapiensMutation(s): 1 
Gene Names: HIST2H3AHIST2H3CH3F2H3FMHIST2H3DH3C15H3C14H3C13
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F106Homo sapiensMutation(s): 1 
Gene Names: 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/EC, G133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFAH2AC4H2AC8
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-JD, H129Homo sapiensMutation(s): 1 
Gene Names: HIST1H2BJH2BFRH2BC11
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (146-MER)I, J146Homo sapiens
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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

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MEXT KAKENHIJapan25116002
JSPS KAKENHIJapan25250023
JSPS KAKENHIJapan26890023

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection, Derived calculations