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 
  • R-Value Observed: 0.177 

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This is version 1.3 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
  • Primary Citation of Related Structures:  
    5JK7

  • 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 of the Cullin4-RING E3 ubiquitin ligase (CRL4) of the host ubiquitin-proteasome-mediated protein degradation pathway ...

    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

    Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA damage-binding protein 1 AB1140Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
NIH Common Fund Data Resources
PHAROS:  Q16531
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein VPRBP CE361Homo sapiensMutation(s): 0 
Gene Names: VPRBPDCAF1KIAA0800RIP
EC: 2.7.11.1
Find proteins for Q9Y4B6 (Homo sapiens)
Explore Q9Y4B6 
Go to UniProtKB:  Q9Y4B6
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PHAROS:  Q9Y4B6
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Uracil-DNA glycosylase DG222Homo sapiensMutation(s): 0 
Gene Names: UNGDGUUNG1UNG15
EC: 3.2.2.27
Find proteins for P13051 (Homo sapiens)
Explore P13051 
Go to UniProtKB:  P13051
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PHAROS:  P13051
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Protein Vpr FH96Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)Mutation(s): 0 
Gene Names: vpr
Find proteins for P12520 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12520 
Go to UniProtKB:  P12520
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.9α = 75.11
b = 128.2β = 89.44
c = 129.2γ = 65.37
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP50GM082251

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-10-19
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence