4CC9

Crystal structure of human SAMHD1 (amino acid residues 582-626) bound to Vpx isolated from sooty mangabey and human DCAF1 (amino acid residues 1058-1396)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Basis of Lentiviral Subversion of a Cellular Protein Degradation Pathway.

Schwefel, D.Groom, H.C.T.Boucherit, V.C.Christodoulou, E.Walker, P.A.Stoye, J.P.Bishop, K.N.Taylor, I.A.

(2014) Nature 505: 234

  • DOI: 10.1038/nature12815
  • Primary Citation of Related Structures:  
    4CC9

  • PubMed Abstract: 
  • Lentiviruses contain accessory genes that have evolved to counteract the effects of host cellular defence proteins that inhibit productive infection. One such restriction factor, SAMHD1, inhibits human immunodeficiency virus (HIV)-1 infection of myeloid-lineage cells as well as resting CD4(+) T cells by reducing the cellular deoxynucleoside 5'-triphosphate (dNTP) concentration to a level at which the viral reverse transcriptase cannot function ...

    Lentiviruses contain accessory genes that have evolved to counteract the effects of host cellular defence proteins that inhibit productive infection. One such restriction factor, SAMHD1, inhibits human immunodeficiency virus (HIV)-1 infection of myeloid-lineage cells as well as resting CD4(+) T cells by reducing the cellular deoxynucleoside 5'-triphosphate (dNTP) concentration to a level at which the viral reverse transcriptase cannot function. In other lentiviruses, including HIV-2 and related simian immunodeficiency viruses (SIVs), SAMHD1 restriction is overcome by the action of viral accessory protein x (Vpx) or the related viral protein r (Vpr) that target and recruit SAMHD1 for proteasomal degradation. The molecular mechanism by which these viral proteins are able to usurp the host cell's ubiquitination machinery to destroy the cell's protection against these viruses has not been defined. Here we present the crystal structure of a ternary complex of Vpx with the human E3 ligase substrate adaptor DCAF1 and the carboxy-terminal region of human SAMHD1. Vpx is made up of a three-helical bundle stabilized by a zinc finger motif, and wraps tightly around the disc-shaped DCAF1 molecule to present a new molecular surface. This adapted surface is then able to recruit SAMHD1 via its C terminus, making it a competent substrate for the E3 ligase to mark for proteasomal degradation. The structure reported here provides a molecular description of how a lentiviral accessory protein is able to subvert the cell's normal protein degradation pathway to inactivate the cellular viral defence system.


    Organizational Affiliation

    Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN VPRBP A361Homo sapiensMutation(s): 0 
Gene Names: DCAF1KIAA0800RIPVPRBP
EC: 2.7.11.1
Find proteins for Q9Y4B6 (Homo sapiens)
Explore Q9Y4B6 
Go to UniProtKB:  Q9Y4B6
NIH Common Fund Data Resources
PHAROS:  Q9Y4B6
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN VPX B119Simian immunodeficiency virusMutation(s): 0 
Find proteins for P19508 (Simian immunodeficiency virus (isolate PBj14/BCL-3))
Explore P19508 
Go to UniProtKB:  P19508
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1 C71Homo sapiensMutation(s): 0 
Gene Names: SAMHD1MOP5
EC: 3.1.5
Find proteins for Q9Y3Z3 (Homo sapiens)
Explore Q9Y3Z3 
Go to UniProtKB:  Q9Y3Z3
NIH Common Fund Data Resources
PHAROS:  Q9Y3Z3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.25α = 90
b = 82.881β = 90
c = 115.561γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
autoSHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2013-12-25
    Changes: Database references
  • Version 1.2: 2014-01-08
    Changes: Database references
  • Version 1.3: 2018-01-24
    Changes: Advisory, Source and taxonomy