3IIF

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

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Literature

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: 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 ...

    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.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Core histone macro-H2A.1, Isoform 1A, B, C211Homo sapiensMutation(s): 0 
Gene Names: H2AFY, MACROH2A1, macroH2A1.1
UniProt
Find proteins for O75367-2 (Homo sapiens)
Explore O75367-2 
Go to UniProtKB:  O75367-2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75367-2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APR
Query on APR
Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]		ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.61α = 90
b = 129.61β = 90
c = 128.29γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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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