4UF3

Deerpox virus DPV022 in complex with Bim BH3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.205 

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.,Sect.D 71: 1593

  • DOI: 10.1107/S1399004715009402
  • Primary Citation of Related Structures:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ANTIAPOPTOTIC MEMBRANE PROTEIN
A
168Deerpox virus (strain Mule deer/United States/W-848-83/1983)Mutation(s): 0 
Gene Names: DPV022
Find proteins for Q08FX8 (Deerpox virus (strain Mule deer/United States/W-848-83/1983))
Go to UniProtKB:  Q08FX8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BCL-2-LIKE PROTEIN 11
B
26Homo sapiensMutation(s): 0 
Gene Names: BCL2L11 (BIM)
Find proteins for O43521 (Homo sapiens)
Go to Gene View: BCL2L11
Go to UniProtKB:  O43521
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.205 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 94.389α = 90.00
b = 94.389β = 90.00
c = 45.541γ = 90.00
Software Package:
Software NamePurpose
SHELXphasing
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-08-12
    Type: Database references
  • Version 1.2: 2015-08-19
    Type: Database references