Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - ABCD 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 74632.84 
• Atom Count: 4341 
• Residue Count: 668 
• Unique protein chains: 4

5KDM

Crystal structure of EBV tegument protein BNRF1 in complex with histone chaperone DAXX and histones H3.3-H4

• DOI: 10.2210/pdb5KDM/pdb

• Classification: CHAPERONE / DNA BINDING PROTEIN
• Organism(s): Homo sapiens, Epstein-Barr virus (strain AG876)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2016-06-08 Released: 2016-09-07 
• Deposition Author(s): Huang, H., Patel, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.5 Å
• R-Value Free: 0.280 
• R-Value Work: 0.234 

Literature

Structural basis underlying viral hijacking of a histone chaperone complex.

Huang, H., Deng, Z., Vladimirova, O., Wiedmer, A., Lu, F., Lieberman, P.M., Patel, D.J.

(2016) Nat Commun 7: 12707-12707

• PubMed: 27581705 

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone H3.3	A	135	Homo sapiens	Mutation(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: 2
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	B	102	Homo sapiens	Mutation(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 Gene View: HIST1H4A HIST1H4B HIST1H4C HIST1H4D HIST1H4E HIST1H4F HIST1H4H HIST1H4I HIST1H4J HIST1H4K HIST1H4L HIST2H4A HIST2H4B HIST4H4 Go to UniProtKB:  P62805

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Death domain-associated protein 6	C	212	Homo sapiens	Mutation(s): 0  Gene Names: DAXX (BING2, DAP6)
Find proteins for Q9UER7 (Homo sapiens) Go to Gene View: DAXX Go to UniProtKB:  Q9UER7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Major tegument protein	D	219	Epstein-Barr virus (strain AG876)	Mutation(s): 0
Find proteins for Q1HVJ0 (Epstein-Barr virus (strain AG876)) Go to UniProtKB:  Q1HVJ0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.5 Å
• R-Value Free: 0.280 
• R-Value Work: 0.234 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 161.216	α = 90.00
b = 161.216	β = 90.00
c = 117.772	γ = 120.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PHASER	phasing
PHENIX	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-06-08 
• Released Date: 2016-09-07 
• Deposition Author(s): Huang, H., Patel, D.

Revision History 

• Version 1.0: 2016-09-07
  Type: Initial release
• Version 1.1: 2018-05-16
  Type: Data collection, Database references, Derived calculations, Source and taxonomy