4UF2

Deerpox virus DPV022 in complex with Bax BH3


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 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • 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. He ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ANTIAPOPTOTIC MEMBRANE PROTEINA168Mule deerpox virusMutation(s): 0 
Find proteins for Q08FX8 (Deerpox virus (strain Mule deer/United States/W-848-83/1983))
Explore Q08FX8 
Go to UniProtKB:  Q08FX8
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
APOPTOSIS REGULATOR BAXB28Homo sapiensMutation(s): 0 
Gene Names: BAXBCL2L4
Find proteins for Q07812 (Homo sapiens)
Explore Q07812 
Go to UniProtKB:  Q07812
NIH Common Fund Data Resources
PHAROS  Q07812
Protein Feature View
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  • Reference Sequence
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 = 92.481α = 90
b = 92.481β = 90
c = 45.529γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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