4HGA

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

• PDB DOI:  https://doi.org/10.2210/pdb4HGA/pdb

• Classification: CHAPERONE/APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-07 Released: 2012-11-07 
• Deposition Author(s): 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.

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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 

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

• PubMed: 23142979 
• DOI: https://doi.org/10.1038/nsmb.2439
• Primary Citation of Related Structures:  
  4HGA


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.91 kDa 
• Atom Count: 3,081 
• Modelled Residue Count: 375 
• Deposited Residue Count: 452 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Death domain-associated protein 6	A	213	Homo sapiens	Mutation(s): 0  Gene Names: DAXX, BING2, DAP6
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UER7 (Homo sapiens) Explore Q9UER7  Go to UniProtKB:  Q9UER7
PHAROS:  Q9UER7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.3	B	136	Homo sapiens	Mutation(s): 0  Gene Names: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B, H3-3A, H3-3B
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens) Explore P84243  Go to UniProtKB:  P84243
PHAROS:  P84243

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	C	103	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4, H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PC4	D [auth A], E [auth A], F [auth A], G [auth B]	TETRACHLOROPLATINATE(II) Cl4 Pt SVZRVTAEYVVVPM-UHFFFAOYSA-J

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 = 72.103	α = 90
b = 72.103	β = 90
c = 323.55	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-07 
Deposition Author(s): 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.

Revision History  

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