1U35

Crystal structure of the nucleosome core particle containing the histone domain of macroH2A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.206 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural characterization of the histone variant macroH2A.

Chakravarthy, S.Gundimella, S.K.Caron, C.Perche, P.Y.Pehrson, J.R.Khochbin, S.Luger, K.

(2005) Mol Cell Biol 25: 7616-7624

  • DOI: https://doi.org/10.1128/MCB.25.17.7616-7624.2005
  • Primary Citation of Related Structures:  
    1U35, 1YD9

  • PubMed Abstract: 

    macroH2A is an H2A variant with a highly unusual structural organization. It has a C-terminal domain connected to the N-terminal histone domain by a linker. Crystallographic and biochemical studies show that changes in the L1 loop in the histone fold region of macroH2A impact the structure and potentially the function of nucleosomes. The 1.6-A X-ray structure of the nonhistone region reveals an alpha/beta fold which has previously been found in a functionally diverse group of proteins. This region associates with histone deacetylases and affects the acetylation status of nucleosomes containing macroH2A. Thus, the unusual domain structure of macroH2A integrates independent functions that are instrumental in establishing a structurally and functionally unique chromatin domain.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, 80523-1870, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1C [auth A],
G [auth E]
136Mus musculusMutation(s): 0 
Gene Names: H3FAH3FCH3FDH3FFH3FHH3FIH3FJH3FKH3FL
UniProt
Find proteins for P68433 (Mus musculus)
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Go to UniProtKB:  P68433
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UniProt GroupP68433
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Hist1h4i proteinD [auth B],
H [auth F]
103Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62806 (Mus musculus)
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IMPC:  MGI:2448443
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UniProt GroupP62806
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
H2A histone familyE [auth C],
I [auth G]
120Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for O75367 (Homo sapiens)
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PHAROS:  O75367
GTEx:  ENSG00000113648 
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UniProt GroupO75367
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
histone 3, H2baF [auth D],
J [auth H]
126Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9D2U9 (Mus musculus)
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UniProt GroupQ9D2U9
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Entity ID: 1
MoleculeChains LengthOrganismImage
alpha-satellite DNAA [auth I],
B [auth J]
146Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.505α = 90
b = 109.598β = 90
c = 175.989γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-09-27
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references
  • Version 1.4: 2023-08-23
    Changes: Data collection, Refinement description