4HGA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.799 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.208 

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

  • 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: DAXX (BING2, DAP6)
Find proteins for Q9UER7 (Homo sapiens)
Go to Gene View: DAXX
Go to UniProtKB:  Q9UER7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.3
B
136Homo sapiensMutation(s): 0 
Gene Names: H3F3A, H3F3B (H3.3A, H3F3, H3.3B)
Find proteins for P84243 (Homo sapiens)
Go to Gene View: H3F3A H3F3B
Go to UniProtKB:  P84243
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H4
C
103Homo sapiensMutation(s): 0 
Gene Names: HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4A, HIST2H4B, HIST4H4 (H4/A, H4FA, H4/I, H4FI, H4/G, H4FG, H4/B, H4FB, H4/J, H4FJ, H4/C, H4FC, H4/H, H4FH, H4/M, H4FM, H4/E, H4FE, H4/D, H4FD, H4/K, H4FK, H4/N, H4F2, H4FN, HIST2H4, H4/O, H4FO)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PC4
Query on PC4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.799 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.208 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 72.103α = 90.00
b = 72.103β = 90.00
c = 323.550γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXmodel building
HKL-2000data scaling
ADSCdata collection
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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