3IID

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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:  

  • 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 a ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Core histone macro-H2A.1, Isoform 1
A
211Homo sapiensMutation(s): 0 
Gene Names: H2AFY (MACROH2A1)
Find proteins for O75367 (Homo sapiens)
Go to Gene View: H2AFY
Go to UniProtKB:  O75367
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APR
Query on APR

Download SDF File 
Download CCD File 
A
ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.176 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 86.260α = 90.00
b = 86.260β = 90.00
c = 51.040γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
ADSCdata collection
XDSdata reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance