Crystal structure of histone H2A.Bbd-H2B dimer

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

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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: https://doi.org/10.1016/j.bbrc.2018.07.114
  • Primary Citation of Related Structures:  

  • 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 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

    University of Science and Technology of China, Hefei, Anhui, 230026, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 2-E,Histone H2A-Bbd type 2/3240Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16778 (Homo sapiens)
Explore Q16778 
Go to UniProtKB:  Q16778
PHAROS:  Q16778
GTEx:  ENSG00000184678 
Find proteins for P0C5Z0 (Homo sapiens)
Explore P0C5Z0 
Go to UniProtKB:  P0C5Z0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0C5Z0Q16778
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • 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
PDB_EXTRACTdata extraction
MOSFLMdata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina--

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description