6FY5

Crystal structure of the macro domain of human macroh2a2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

MacroH2A histone variants limit chromatin plasticity through two distinct mechanisms.

Kozlowski, M.Corujo, D.Hothorn, M.Guberovic, I.Mandemaker, I.K.Blessing, C.Sporn, J.Gutierrez-Triana, A.Smith, R.Portmann, T.Treier, M.Scheffzek, K.Huet, S.Timinszky, G.Buschbeck, M.Ladurner, A.G.

(2018) EMBO Rep 19

  • DOI: 10.15252/embr.201744445
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • MacroH2A histone variants suppress tumor progression and act as epigenetic barriers to induced pluripotency. How they impart their influence on chromatin plasticity is not well understood. Here, we analyze how the different domains of macroH2A proteins contribute to chromatin structure and dynamics ...

    MacroH2A histone variants suppress tumor progression and act as epigenetic barriers to induced pluripotency. How they impart their influence on chromatin plasticity is not well understood. Here, we analyze how the different domains of macroH2A proteins contribute to chromatin structure and dynamics. By solving the crystal structure of the macrodomain of human macroH2A2 at 1.7 Å, we find that its putative binding pocket exhibits marked structural differences compared with the macroH2A1.1 isoform, rendering macroH2A2 unable to bind ADP-ribose. Quantitative binding assays show that this specificity is conserved among vertebrate macroH2A isoforms. We further find that macroH2A histones reduce the transient, PARP1-dependent chromatin relaxation that occurs in living cells upon DNA damage through two distinct mechanisms. First, macroH2A1.1 mediates an isoform-specific effect through its ability to suppress PARP1 activity. Second, the unstructured linker region exerts an additional repressive effect that is common to all macroH2A proteins. In the absence of DNA damage, the macroH2A linker is also sufficient for rescuing heterochromatin architecture in cells deficient for macroH2A.


    Organizational Affiliation

    Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität München, Munich, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Core histone macro-H2A.2A, B198Homo sapiensMutation(s): 0 
Gene Names: H2AFY2MACROH2A2
Find proteins for Q9P0M6 (Homo sapiens)
Explore Q9P0M6 
Go to UniProtKB:  Q9P0M6
NIH Common Fund Data Resources
PHAROS  Q9P0M6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.75α = 90
b = 41.37β = 97.05
c = 84.15γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-03-10 
  • Released Date: 2018-04-04 
  • Deposition Author(s): Hothorn, M.

Revision History 

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2018-09-12
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-17
    Changes: Data collection, Database references, Structure summary