4UF1 | pdb_00004uf1

Deerpox virus DPV022 in complex with Bak BH3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.206 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

Validation slider image for 4UF1

This is version 2.2 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: https://doi.org/10.1107/S1399004715009402
  • Primary Citation 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.


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

Macromolecule Content 

  • Total Structure Weight: 22.61 kDa 
  • Atom Count: 1,319 
  • Modeled Residue Count: 157 
  • Deposited Residue Count: 194 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Antiapoptotic membrane protein168Deerpox virus W-1170-84Mutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08FX8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Bcl-2 homologous antagonist/killer26Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16611 (Homo sapiens)
Explore Q16611 
Go to UniProtKB:  Q16611
PHAROS:  Q16611
GTEx:  ENSG00000030110 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16611
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.206 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.26α = 90
b = 93.26β = 90
c = 45.62γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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 2.0: 2019-10-23
    Changes: Atomic model, Data collection, Other
  • Version 2.1: 2021-06-30
    Changes: Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 2.2: 2024-05-01
    Changes: Data collection, Database references, Refinement description