6XQI

Structure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A.

Byeon, I.L.Calero, G.Wu, Y.Byeon, C.H.Jung, J.DeLucia, M.Zhou, X.Weiss, S.Ahn, J.Hao, C.Skowronski, J.Gronenborn, A.M.

(2021) Nat Commun 12: 6864-6864

  • DOI: https://doi.org/10.1038/s41467-021-27009-w
  • Primary Citation of Related Structures:  
    6XQI, 6XQJ

  • PubMed Abstract: 

    HIV-1 Vpr is a prototypic member of a large family of structurally related lentiviral virulence factors that antagonize various aspects of innate antiviral immunity. It subverts host cell DNA repair and protein degradation machineries by binding and inhibiting specific post-replication repair enzymes, linking them via the DCAF1 substrate adaptor to the Cullin 4 RING E3 ligase (CRL4 DCAF1 ). HIV-1 Vpr also binds to the multi-domain protein hHR23A, which interacts with the nucleotide excision repair protein XPC and shuttles ubiquitinated proteins to the proteasome. Here, we report the atomic resolution structure of Vpr in complex with the C-terminal half of hHR23A, containing the XPC-binding (XPCB) and ubiquitin-associated (UBA2) domains. The XPCB and UBA2 domains bind to different sides of Vpr's 3-helix-bundle structure, with UBA2 interacting with the α2 and α3 helices of Vpr, while the XPCB domain contacts the opposite side of Vpr's α3 helix. The structure as well as biochemical results reveal that hHR23A and DCAF1 use overlapping binding surfaces on Vpr, even though the two proteins exhibit entirely different three-dimensional structures. Our findings show that Vpr independently targets hHR23A- and DCAF1- dependent pathways and highlight HIV-1 Vpr as a versatile module that interferes with DNA repair and protein degradation pathways.


  • Organizational Affiliation

    Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein Vpr
A, B, C, D
64Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)Mutation(s): 0 
Gene Names: vpr
UniProt
Find proteins for P12520 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12520 
Go to UniProtKB:  P12520
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12520
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
UV excision repair protein RAD23 homolog AE [auth F],
F [auth G]
40Homo sapiensMutation(s): 0 
Gene Names: RAD23A
UniProt & NIH Common Fund Data Resources
Find proteins for P54725 (Homo sapiens)
Explore P54725 
Go to UniProtKB:  P54725
PHAROS:  P54725
GTEx:  ENSG00000179262 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54725
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ASN-PRO-LEU-GLU-PHE-LEUG [auth H],
H [auth I]
6Homo sapiensMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.165α = 90
b = 130.165β = 90
c = 81.305γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP50AI150481

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-11
    Type: Initial release
  • Version 1.1: 2021-12-08
    Changes: Database references