4NFT

Crystal structure of human lnkH2B-h2A.Z-Anp32e

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Anp32e, a higher eukaryotic histone chaperone directs preferential recognition for H2A.Z

Mao, Z., Pan, L., Wang, W., Sun, J., Shan, S., Dong, Q., Liang, X., Dai, L., Ding, X., Chen, S., Zhang, Z., Zhu, B., Zhou, Z.

(2014) Cell Res. 24: 389-399

  • DOI: 10.1038/cr.2014.30

  • PubMed Abstract: 

    • H2A.Z is a highly conserved histone variant in all species. The chromatin deposition of H2A.Z is specifically catalyzed by the yeast chromatin remodeling complex SWR1 and its mammalian counterpart SRCAP. However, the mechanism by which H2A.Z is prefe ...

    H2A.Z is a highly conserved histone variant in all species. The chromatin deposition of H2A.Z is specifically catalyzed by the yeast chromatin remodeling complex SWR1 and its mammalian counterpart SRCAP. However, the mechanism by which H2A.Z is preferentially recognized by non-histone proteins remains elusive. Here we identified Anp32e, a novel higher eukaryote-specific histone chaperone for H2A.Z. Anp32e preferentially associates with H2A.Z-H2B dimers rather than H2A-H2B dimers in vitro and in vivo and dissociates non-nucleosomal aggregates formed by DNA and H2A-H2B. We determined the crystal structure of the Anp32e chaperone domain (186-232) in complex with the H2A.Z-H2B dimer. In this structure, the region containing Anp32e residues 214-224, which is absent in other Anp32 family proteins, specifically interacts with the extended H2A.Z αC helix, which exhibits an unexpected conformational change. Genome-wide profiling of Anp32e revealed a remarkable co-occupancy between Anp32e and H2A.Z. Cells overexpressing Anp32e displayed a strong global H2A.Z loss at the +1 nucleosomes, whereas cells depleted of Anp32e displayed a moderate global H2A.Z increase at the +1 nucleosomes. This suggests that Anp32e may help to resolve the non-nucleosomal H2A.Z aggregates and also facilitate the removal of H2A.Z at the +1 nucleosomes, and the latter may help RNA polymerase II to pass the first nucleosomal barrier.

    Organizational Affiliation: 

    1] Graduate Program, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China [2] National Institute of Biological Sciences, Beijing 102206, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 2-E, Histone H2A.Z
A, B, C, D
209Homo sapiensMutation(s): 0 
Gene Names: H2AFZ (H2AZ), HIST2H2BE (H2BFQ)
Find proteins for P0C0S5 (Homo sapiens)
Go to Gene View: H2AFZ
Go to UniProtKB:  P0C0S5
Find proteins for Q16778 (Homo sapiens)
Go to Gene View: HIST2H2BE
Go to UniProtKB:  Q16778
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Acidic leucine-rich nuclear phosphoprotein 32 family member E
E, F
52Homo sapiensMutation(s): 0 
Gene Names: ANP32E
Find proteins for Q9BTT0 (Homo sapiens)
Go to Gene View: ANP32E
Go to UniProtKB:  Q9BTT0
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 76.412α = 90.00
b = 104.297β = 99.15
c = 124.743γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
ADSCdata collection
PHENIXrefinement
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2015-09-23
    Type: Database references
  • Version 1.2: 2017-08-16
    Type: Refinement description, Source and taxonomy