Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 22.79 kDa 
• Atom Count: 1260 
• Modelled Residue Count: 155 
• Deposited Residue Count: 196 
• Unique protein chains: 2

4UF2

Deerpox virus DPV022 in complex with Bax BH3

• DOI: 10.2210/pdb4UF2/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Deerpox virus W-1170-84, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-23 Released: 2015-08-05 
• Deposition Author(s): Burton, D.R., Kvansakul, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.274 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 

Literature

Structural Basis of Deerpox Virus-Mediated Inhibition of Apoptosis.

Burton, D.R., Caria, S., Marshall, B., Barry, M., Kvansakul, M.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1593

• PubMed: 26249341 
• DOI: 10.1107/S1399004715009402
• Primary Citation of Related Structures:  
  4UF1, 4UF2, 4UF3


• PubMed Abstract: 
  

Apoptosis is a key innate defence mechanism to eliminate virally infected cells. To counteract premature host-cell apoptosis, poxviruses have evolved numerous molecular strategies, including the use of Bcl-2 proteins, to ensure their own survival. Here, it is reported that the Deerpox virus inhibitor of apoptosis, DPV022, only engages a highly restricted set of death-inducing Bcl-2 proteins, including Bim, Bax and Bak, with modest affinities. Structural analysis reveals that DPV022 adopts a Bcl-2 fold with a dimeric domain-swapped topology and binds pro-death Bcl-2 proteins via two conserved ligand-binding grooves found on opposite sides of the dimer. Structures of DPV022 bound to Bim, Bak and Bax BH3 domains reveal that a partial obstruction of the binding groove is likely to be responsible for the modest affinities of DPV022 for BH3 domains. These findings reveal that domain-swapped dimeric Bcl-2 folds are not unusual and may be found more widely in viruses. Furthermore, the modest affinities of DPV022 for pro-death Bcl-2 proteins suggest that two distinct classes of anti-apoptotic viral Bcl-2 proteins exist: those that are monomeric and tightly bind a range of death-inducing Bcl-2 proteins, and others such as DPV022 that are dimeric and only bind a very limited number of death-inducing Bcl-2 proteins with modest affinities.

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Organizational Affiliation: 

Department of Biochemistry, La Trobe University, Melbourne, VIC 3058, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antiapoptotic membrane protein	A	168	Deerpox virus W-1170-84	Mutation(s): 0  Gene Names: DpV84gp022
UniProt
Find proteins for Q08FX8 (Deerpox virus (strain Mule deer/United States/W-848-83/1983)) Explore Q08FX8  Go to UniProtKB:  Q08FX8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptosis regulator BAX	B	28	Homo sapiens	Mutation(s): 0  Gene Names: BAX, BCL2L4
UniProt & NIH Common Fund Data Resources
Find proteins for Q07812 (Homo sapiens) Explore Q07812  Go to UniProtKB:  Q07812
PHAROS:  Q07812 GTEx:  ENSG00000087088

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.274 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.481	α = 90
b = 92.481	β = 90
c = 45.529	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-12-23 
• Released Date: 2015-08-05 
Deposition Author(s): Burton, D.R., Kvansakul, M.

Revision History  

• Version 1.0: 2015-08-05
  Type: Initial release
  
• Version 1.1: 2015-08-12
  Changes: Database references
• Version 1.2: 2015-08-19
  Changes: Database references
• Version 1.3: 2021-06-30
  Changes: Database references, Other, Source and taxonomy, Structure summary