Crystal structure of the macro-domain of human core histone variant macroH2A1.2

Experimental Data Snapshot

  • Resolution: 2.92 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Splicing regulates NAD metabolite binding to histone macroH2A.

Kustatscher, G.Hothorn, M.Pugieux, C.Scheffzek, K.Ladurner, A.G.

(2005) Nat Struct Mol Biol 12: 624-625

  • DOI: https://doi.org/10.1038/nsmb956
  • Primary Citation of Related Structures:  
    1ZR5, 2FXK

  • PubMed Abstract: 

    Histone macroH2A is a hallmark of mammalian heterochromatin. Here we show that human macroH2A1.1 binds the SirT1-metabolite O-acetyl-ADP-ribose (OAADPR) through its macro domain. The 1.6-A crystal structure and mutants reveal how the metabolite is recognized. Mutually exclusive exon use in the gene H2AFY produces macroH2A1.2, whose tissue distribution differs. MacroH2A1.2 shows only subtle structural changes but cannot bind nucleotides. Alternative splicing may thus regulate the binding of nicotinamide adenine dinucleotide (NAD) metabolites to chromatin.

  • Organizational Affiliation

    Gene Expression Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
H2AFY protein
A, B
214Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O75367 (Homo sapiens)
Explore O75367 
Go to UniProtKB:  O75367
GTEx:  ENSG00000113648 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75367
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.92 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.549α = 90
b = 72.258β = 90
c = 144.641γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Refinement description