4UF1

Deerpox virus DPV022 in complex with Bak BH3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 2.0 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.,Li Ka Shing Institute for Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2S2, Canada.




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 HOMOLOGOUS ANTAGONIST/KILLER
B
26Homo sapiensMutation(s): 0 
Gene Names: BAK1 (BAK, BCL2L7, CDN1)
Find proteins for Q16611 (Homo sapiens)
Go to Gene View: BAK1
Go to UniProtKB:  Q16611
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.178 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 93.260α = 90.00
b = 93.260β = 90.00
c = 45.620γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement

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
  • Version 2.0: 2019-10-23
    Type: Atomic model, Data collection, Other