2XPX | pdb_00002xpx

Crystal structure of BHRF1:Bak BH3 complex

• PDB DOI: https://doi.org/10.2210/pdb2XPX/pdb

• Classification: APOPTOSIS
• Organism(s): human gammaherpesvirus 4, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-08-31 Released: 2011-01-26 
• Deposition Author(s): Kvansakul, M., Huang, D.C.S., Colman, P.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Structural Basis for Apoptosis Inhibition by Epstein-Barr Virus Bhrf1.

Kvansakul, M., Wei, A.H., Fletcher, J.I., Willis, S.N., Chen, L., Roberts, A.W., Huang, D.C.S., Colman, P.M.

(2010) PLoS Pathog 6: 1236

• PubMed: 21203485 
• DOI: https://doi.org/10.1371/journal.ppat.1001236
• Primary Citation Related Structures: 
  2V6Q, 2WH6, 2XPX


• PubMed Abstract: 
  

  Epstein-Barr virus (EBV) is associated with human malignancies, especially those affecting the B cell compartment such as Burkitt lymphoma. The virally encoded homolog of the mammalian pro-survival protein Bcl-2, BHRF1 contributes to viral infectivity and lymphomagenesis. In addition to the pro-apoptotic BH3-only protein Bim, its key target in lymphoid cells, BHRF1 also binds a selective sub-set of pro-apoptotic proteins (Bid, Puma, Bak) expressed by host cells. A consequence of BHRF1 expression is marked resistance to a range of cytotoxic agents and in particular, we show that its expression renders a mouse model of Burkitt lymphoma untreatable. As current small organic antagonists of Bcl-2 do not target BHRF1, the structures of it in complex with Bim or Bak shown here will be useful to guide efforts to target BHRF1 in EBV-associated malignancies, which are usually associated with poor clinical outcomes.

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Organizational Affiliation: 
• The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 23.1 kDa 
• Atom Count: 1,534 
• Modeled Residue Count: 176 
• Deposited Residue Count: 199 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
APOPTOSIS REGULATOR BHRF1	A	173	human gammaherpesvirus 4	Mutation(s): 0
UniProt
Find proteins for P03182 (Epstein-Barr virus (strain B95-8)) Explore P03182  Go to UniProtKB:  P03182

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BCL-2 HOMOLOGOUS ANTAGONIST/KILLER	B	26	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q16611 (Homo sapiens) Explore Q16611  Go to UniProtKB:  Q16611
PHAROS:  Q16611 GTEx:  ENSG00000030110

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	C [auth A], D [auth A], E [auth A], F [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.387	α = 90
b = 62.387	β = 90
c = 93.729	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-26 
Deposition Author(s): Kvansakul, M., Huang, D.C.S., Colman, P.M.

Revision History  

• Version 1.0: 2011-01-26
  Type: Initial release
  
• Version 1.1: 2011-12-28
  Changes: Database references, Version format compliance
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description