6A7U

Crystal structure of histone H2A.Bbd-H2B dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

wwPDB Validation 3D Report Full Report



Literature

Crystal structure of the histone heterodimer containing histone variant H2A.Bbd.

Dai, L.Xie, X.Zhou, Z.

(2018) Biochem Biophys Res Commun 503: 1786-1791

  • DOI: 10.1016/j.bbrc.2018.07.114
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • H2A.Bbd, the most divergent histone variant among all known H2A type histones, is involved in gene transcription, spermiogenesis, DNA replication and RNA splicing. Incorporation of H2A.Bbd-H2B dimer, a fundamental unit of H2A.Bbd nucleosome, modulate ...

    H2A.Bbd, the most divergent histone variant among all known H2A type histones, is involved in gene transcription, spermiogenesis, DNA replication and RNA splicing. Incorporation of H2A.Bbd-H2B dimer, a fundamental unit of H2A.Bbd nucleosome, modulate structures of nucleosome or chromatin, but the underlying mechanism remains elusive. Here we determined a crystal structure of H2A.Bbd-H2B dimer at 2.6 Å resolution. Although the H2A.Bbd-H2B dimer structure largely resembles that of H2A-H2B, substitution of H2A αC helix residues by H2A.Bbd counterparts lead to the transition of a long αC-helix to the short 3 10 -helix, likely owing to the rearrangement of the hydrogen-bond network. Moreover, structural comparison revealed a strikingly altered electrostatic potential surface for H2A.Bbd-H2B dimer displaying a diminished DNA binding capability. Our study provides the first high-resolution structure of histone variant H2A.Bbd and shed a light on biological function of H2A.Bbd.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China. Electronic address: zhouzh@ibp.ac.cn.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 2-E,Histone H2A-Bbd type 2/3
A
240Homo sapiensMutation(s): 0 
Gene Names: HIST2H2BEH2BFQ
Find proteins for Q16778 (Homo sapiens)
Go to UniProtKB:  Q16778
NIH Common Fund Data Resources
PHAROS  Q16778
Find proteins for P0C5Z0 (Homo sapiens)
Go to UniProtKB:  P0C5Z0
NIH Common Fund Data Resources
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.64α = 90
b = 141.91β = 90
c = 56.91γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-07-04 
  • Released Date: 2019-02-27 
  • Deposition Author(s): Dai, L., Zhou, Z.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina--

Revision History 

  • Version 1.0: 2019-02-27
    Type: Initial release