4CAY

Crystal structure of a human Anp32e-H2A.Z-H2B complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Anp32E is a Histone Chaperone that Removes H2A.Z from Chromatin

Obri, A.Ouararhni, K.Papin, C.Diebold, M.-L.Padmanabhan, K.Marek, M.Stoll, I.Roy, L.Reilly, P.T.Wak, T.W.Dimitrov, S.Romier, C.Hamiche, A.

(2014) Nature 648: 505

  • DOI: 10.1038/nature12922
  • Primary Citation of Related Structures:  
    4CAY

  • PubMed Abstract: 
  • H2A.Z is an essential histone variant implicated in the regulation of key nuclear events. However, the metazoan chaperones responsible for H2A.Z deposition and its removal from chromatin remain unknown. Here we report the identification and character ...

    H2A.Z is an essential histone variant implicated in the regulation of key nuclear events. However, the metazoan chaperones responsible for H2A.Z deposition and its removal from chromatin remain unknown. Here we report the identification and characterization of the human protein ANP32E as a specific H2A.Z chaperone. We show that ANP32E is a member of the presumed H2A.Z histone-exchange complex p400/TIP60. ANP32E interacts with a short region of the docking domain of H2A.Z through a new motif termed H2A.Z interacting domain (ZID). The 1.48 Å resolution crystal structure of the complex formed between the ANP32E-ZID and the H2A.Z/H2B dimer and biochemical data support an underlying molecular mechanism for H2A.Z/H2B eviction from the nucleosome and its stabilization by ANP32E through a specific extension of the H2A.Z carboxy-terminal α-helix. Finally, analysis of H2A.Z localization in ANP32E(-/-) cells by chromatin immunoprecipitation followed by sequencing shows genome-wide enrichment, redistribution and accumulation of H2A.Z at specific chromatin control regions, in particular at enhancers and insulators.


    Organizational Affiliation

    Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS, INSERM, 1 rue Laurent Fries, B.P. 10142, 67404 Illkirch Cedex, France.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE H2A.ZA111Homo sapiensMutation(s): 0 
Gene Names: H2AZ1H2AFZH2AZ
Find proteins for P0C0S5 (Homo sapiens)
Explore P0C0S5 
Go to UniProtKB:  P0C0S5
NIH Common Fund Data Resources
PHAROS  P0C0S5
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE H2B TYPE 1-JB97Homo sapiensMutation(s): 0 
Gene Names: H2BC11H2BFRHIST1H2BJ
Find proteins for P06899 (Homo sapiens)
Explore P06899 
Go to UniProtKB:  P06899
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PHAROS  P06899
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER EC30Homo sapiensMutation(s): 0 
Gene Names: ANP32E
Find proteins for Q9BTT0 (Homo sapiens)
Explore Q9BTT0 
Go to UniProtKB:  Q9BTT0
NIH Common Fund Data Resources
PHAROS  Q9BTT0
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.816α = 90
b = 66.076β = 95.76
c = 45.293γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references
  • Version 1.2: 2014-03-19
    Changes: Structure summary
  • Version 1.3: 2016-03-09
    Changes: Structure summary
  • Version 1.4: 2016-12-14
    Changes: Structure summary