7P0U | pdb_00007p0u

ORF virus encoded Bcl-2 homolog ORFV125 in complex with Puma BH3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 
    0.274 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7P0U

This is version 1.3 of the entry. See complete history

Literature

Structural Investigation of Orf Virus Bcl-2 Homolog ORFV125 Interactions with BH3-Motifs from BH3-Only Proteins Puma and Hrk.

Suraweera, C.D.Hinds, M.G.Kvansakul, M.

(2021) Viruses 13

  • DOI: https://doi.org/10.3390/v13071374
  • Primary Citation Related Structures: 
    7P0S, 7P0U

  • PubMed Abstract: 

    Numerous viruses have evolved sophisticated countermeasures to hijack the early programmed cell death of host cells in response to infection, including the use of proteins homologous in sequence or structure to Bcl-2. Orf virus, a member of the parapoxviridae , encodes for the Bcl-2 homolog ORFV125, a potent inhibitor of Bcl-2-mediated apoptosis in the host. ORFV125 acts by directly engaging host proapoptotic Bcl-2 proteins including Bak and Bax as well as the BH3-only proteins Hrk and Puma. Here, we determined the crystal structures of ORFV125 bound to the BH3 motif of proapoptotic proteins Puma and Hrk. The structures reveal that ORFV125 engages proapoptotic BH3 motif peptides using the canonical ligand binding groove. An Arg located in the structurally equivalent BH1 region of ORFV125 forms an ionic interaction with the conserved Asp in the BH3 motif in a manner that mimics the canonical ionic interaction seen in host Bcl-2:BH3 motif complexes. These findings provide a structural basis for Orf virus-mediated inhibition of host cell apoptosis and reveal the flexibility of virus encoded Bcl-2 proteins to mimic key interactions from endogenous host signalling pathways.


  • Organizational Affiliation
    • La Trobe Institute for Molecular Science, Department of Biochemistry and Genetics, La Trobe University, Melbourne, VIC 3086, Australia.

Macromolecule Content 

  • Total Structure Weight: 77.12 kDa 
  • Atom Count: 4,869 
  • Modeled Residue Count: 616 
  • Deposited Residue Count: 696 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Apoptosis inhibitorA,
C [auth B],
E [auth D],
G [auth F]
148Orf virusMutation(s): 0 
Gene Names: ORFV125ORF125
UniProt
Find proteins for A0A0R8HV90 (Orf virus)
Explore A0A0R8HV90 
Go to UniProtKB:  A0A0R8HV90
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0R8HV90
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Activator of apoptosis harakiriB [auth U],
D [auth C],
F [auth E],
H [auth G]
26Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O00198 (Homo sapiens)
Explore O00198 
Go to UniProtKB:  O00198
PHAROS:  O00198
GTEx:  ENSG00000135116 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00198
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
K [auth A],
L [auth A],
O [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
M [auth A],
N [auth B],
P [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.274 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.405α = 71.884
b = 57.697β = 76.607
c = 65.063γ = 75.085
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaFT130101349

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary