5AJA

Crystal structure of mandrill SAMHD1 (amino acid residues 1-114) bound to Vpx isolated from mandrill and human DCAF1 (amino acid residues 1058-1396)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

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This is version 1.0 of the entry. See complete history


Literature

Molecular Determinants for Recognition of Divergent Samhd1 Proteins by the Lentiviral Accessory Protein Vpx.

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

(2015) Cell Host Microbe 17: 489

  • DOI: 10.1016/j.chom.2015.03.004
  • Primary Citation of Related Structures:  
    5AJA

  • PubMed Abstract: 
  • The SAMHD1 triphosphohydrolase inhibits HIV-1 infection of myeloid and resting T cells by depleting dNTPs. To overcome SAMHD1, HIV-2 and some SIVs encode either of two lineages of the accessory protein Vpx that bind the SAMHD1 N or C terminus and redirect the host cullin-4 ubiquitin ligase to target SAMHD1 for proteasomal degradation ...

    The SAMHD1 triphosphohydrolase inhibits HIV-1 infection of myeloid and resting T cells by depleting dNTPs. To overcome SAMHD1, HIV-2 and some SIVs encode either of two lineages of the accessory protein Vpx that bind the SAMHD1 N or C terminus and redirect the host cullin-4 ubiquitin ligase to target SAMHD1 for proteasomal degradation. We present the ternary complex of Vpx from SIV that infects mandrills (SIVmnd-2) with the cullin-4 substrate receptor, DCAF1, and N-terminal and SAM domains from mandrill SAMHD1. The structure reveals details of Vpx lineage-specific targeting of SAMHD1 N-terminal "degron" sequences. Comparison with Vpx from SIV that infects sooty mangabeys (SIVsmm) complexed with SAMHD1-DCAF1 identifies molecular determinants directing Vpx lineages to N- or C-terminal SAMHD1 sequences. Inspection of the Vpx-DCAF1 interface also reveals conservation of Vpx with the evolutionally related HIV-1/SIV accessory protein Vpr. These data suggest a unified model for how Vpx and Vpr exploit DCAF1 to promote viral replication.


    Organizational Affiliation

    Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK. Electronic address: itaylor@nimr.mrc.ac.uk.



Macromolecules
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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
VPX PROTEIN B102Simian immunodeficiency virusMutation(s): 0 
Gene Names: vpxvpr
Find proteins for Q7ZB17 (Simian immunodeficiency virus)
Explore Q7ZB17 
Go to UniProtKB:  Q7ZB17
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SAM DOMAIN AND HD DOMAIN-CONTAINING PROTEIN C117Mandrillus sphinxMutation(s): 0 
Gene Names: SAMHD1
Find proteins for H6WEA4 (Mandrillus sphinx)
Explore H6WEA4 
Go to UniProtKB:  H6WEA4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 2.65 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.021α = 90
b = 102.021β = 90
c = 265.001γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-22
    Type: Initial release