5JK7

The X-ray structure of the DDB1-DCAF1-Vpr-UNG2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The DDB1-DCAF1-Vpr-UNG2 crystal structure reveals how HIV-1 Vpr steers human UNG2 toward destruction.

Wu, Y.Zhou, X.Barnes, C.O.DeLucia, M.Cohen, A.E.Gronenborn, A.M.Ahn, J.Calero, G.

(2016) Nat.Struct.Mol.Biol. 23: 933-940

  • DOI: 10.1038/nsmb.3284

  • PubMed Abstract: 
  • The HIV-1 accessory protein Vpr is required for efficient viral infection of macrophages and promotion of viral replication in T cells. Vpr's biological activities are closely linked to the interaction with human DCAF1, a cellular substrate receptor ...

    The HIV-1 accessory protein Vpr is required for efficient viral infection of macrophages and promotion of viral replication in T cells. Vpr's biological activities are closely linked to the interaction with human DCAF1, a cellular substrate receptor of the Cullin4-RING E3 ubiquitin ligase (CRL4) of the host ubiquitin-proteasome-mediated protein degradation pathway. The molecular details of how Vpr usurps the protein degradation pathway have not been delineated. Here we present the crystal structure of the DDB1-DCAF1-HIV-1-Vpr-uracil-DNA glycosylase (UNG2) complex. The structure reveals how Vpr engages with DCAF1, creating a binding interface for UNG2 recruitment in a manner distinct from the recruitment of SAMHD1 by Vpx proteins. Vpr and Vpx use similar N-terminal and helical regions to bind the substrate receptor, whereas different regions target the specific cellular substrates. Furthermore, Vpr uses molecular mimicry of DNA by a variable loop for specific recruitment of the UNG2 substrate.


    Organizational Affiliation

    Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, California, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA damage-binding protein 1
A, B
1140Homo sapiensMutation(s): 0 
Gene Names: DDB1 (XAP1)
Find proteins for Q16531 (Homo sapiens)
Go to Gene View: DDB1
Go to UniProtKB:  Q16531
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein VPRBP
C, E
361Homo sapiensMutation(s): 0 
Gene Names: DCAF1 (KIAA0800, RIP, VPRBP)
Find proteins for Q9Y4B6 (Homo sapiens)
Go to Gene View: DCAF1
Go to UniProtKB:  Q9Y4B6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Uracil-DNA glycosylase
D, G
222Homo sapiensMutation(s): 0 
Gene Names: UNG (DGU, UNG1, UNG15)
EC: 3.2.2.27
Find proteins for P13051 (Homo sapiens)
Go to Gene View: UNG
Go to UniProtKB:  P13051
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Protein Vpr
F, H
96Human immunodeficiency virus type 1 group M subtype B (isolate NY5)Mutation(s): 0 
Gene Names: vpr
Find proteins for P12520 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Go to UniProtKB:  P12520
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.176 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 119.900α = 75.11
b = 128.200β = 89.44
c = 129.200γ = 65.37
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP50GM082251

Revision History 

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-10-19
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Derived calculations