Crystal structure of the macro domain of human histone macroH2A1.1 in complex with ADP-ribose (form A)

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

Starting Model: experimental
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A macrodomain-containing histone rearranges chromatin upon sensing PARP1 activation.

Timinszky, G.Till, S.Hassa, P.O.Hothorn, M.Kustatscher, G.Nijmeijer, B.Colombelli, J.Altmeyer, M.Stelzer, E.H.Scheffzek, K.Hottiger, M.O.Ladurner, A.G.

(2009) Nat Struct Mol Biol 16: 923-929

  • DOI: https://doi.org/10.1038/nsmb.1664
  • Primary Citation of Related Structures:  
    3IID, 3IIF

  • PubMed Abstract: 

    Poly-ADP-ribosylation is a post-translational modification catalyzed by PARP enzymes with roles in transcription and chromatin biology. Here we show that distinct macrodomains, including those of histone macroH2A1.1, are recruited to sites of PARP1 activation induced by laser-generated DNA damage. Chemical PARP1 inhibitors, PARP1 knockdown and mutation of ADP-ribose-binding residues in macroH2A1.1 abrogate macrodomain recruitment. Notably, histone macroH2A1.1 senses PARP1 activation, transiently compacts chromatin, reduces the recruitment of DNA damage factor Ku70-Ku80 and alters gamma-H2AX patterns, whereas the splice variant macroH2A1.2, which is deficient in poly-ADP-ribose binding, does not mediate chromatin rearrangements upon PARP1 activation. The structure of the macroH2A1.1 macrodomain in complex with ADP-ribose establishes a poly-ADP-ribose cap-binding function and reveals conformational changes in the macrodomain upon ligand binding. We thus identify macrodomains as modules that directly sense PARP activation in vivo and establish macroH2A histones as dynamic regulators of chromatin plasticity.

  • Organizational Affiliation

    Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Core histone macro-H2A.1, Isoform 1211Homo sapiensMutation(s): 0 
Gene Names: H2AFYMACROH2A1macroH2A1.1
UniProt & NIH Common Fund Data Resources
Find proteins for O75367-2 (Homo sapiens)
Explore O75367-2 
Go to UniProtKB:  O75367-2
GTEx:  ENSG00000113648 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75367-2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on APR

Download Ideal Coordinates CCD File 
C15 H23 N5 O14 P2
Query on NO3

Download Ideal Coordinates CCD File 
N O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.26α = 90
b = 86.26β = 90
c = 51.04γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description