4HGA

Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX.

Liu, C.P.Xiong, C.Y.Wang, M.Z.Yu, Z.L.Yang, N.Chen, P.Zhang, Z.G.Li, G.H.Xu, R.M.

(2012) Nat Struct Mol Biol 19: 1287-1292

  • DOI: 10.1038/nsmb.2439
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Mammalian histone H3.3 is a variant of the canonical H3.1 essential for genome reprogramming in fertilized eggs and maintenance of chromatin structure in neuronal cells. An H3.3-specific histone chaperone, DAXX, directs the deposition of H3.3 onto pe ...

    Mammalian histone H3.3 is a variant of the canonical H3.1 essential for genome reprogramming in fertilized eggs and maintenance of chromatin structure in neuronal cells. An H3.3-specific histone chaperone, DAXX, directs the deposition of H3.3 onto pericentric and telomeric heterochromatin. H3.3 differs from H3.1 by only five amino acids, yet DAXX can distinguish the two with high precision. By a combination of structural, biochemical and cell-based targeting analyses, we show that Ala87 and Gly90 are the principal determinants of human H3.3 specificity. DAXX uses a shallow hydrophobic pocket to accommodate the small hydrophobic Ala87 of H3.3, whereas a polar binding environment in DAXX prefers Gly90 in H3.3 over the hydrophobic Met90 in H3.1. An H3.3-H4 heterodimer is bound by the histone-binding domain of DAXX, which makes extensive contacts with both H3.3 and H4.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Death domain-associated protein 6
A
213Homo sapiensMutation(s): 0 
Gene Names: DAXXBING2DAP6
Find proteins for Q9UER7 (Homo sapiens)
Go to UniProtKB:  Q9UER7
NIH Common Fund Data Resources
PHAROS  Q9UER7

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.3
B
136Homo sapiensMutation(s): 0 
Gene Names: H3F3AH3.3AH3F3PP781H3F3BH3.3BH3-3AH3-3B
Find proteins for P84243 (Homo sapiens)
Go to UniProtKB:  P84243
NIH Common Fund Data Resources
PHAROS  P84243

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H4
C
103Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS  P62805
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PC4
Query on PC4

Download CCD File 
A, B
TETRACHLOROPLATINATE(II)
Cl4 Pt
SVZRVTAEYVVVPM-UHFFFAOYSA-J
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.103α = 90
b = 72.103β = 90
c = 323.55γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2014-09-10
    Changes: Database references