5AJA | pdb_00005aja

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

• PDB DOI: https://doi.org/10.2210/pdb5AJA/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Homo sapiens, Simian immunodeficiency virus, Mandrillus sphinx
• Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-02-20 Released: 2015-04-22 
• Deposition Author(s): Schwefel, D., Boucherit, V.C., Christodoulou, E., Walker, P.A., Stoye, J.P., Bishop, K.N., Taylor, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.227 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

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

• PubMed: 25856754 
• DOI: https://doi.org/10.1016/j.chom.2015.03.004
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.
Division of Virology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.
Division of Virology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK; Faculty of Medicine, Imperial College London, London SW7 2AZ, UK.
Division of Virology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK. Electronic address: [e-mail].
Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 65.99 kDa 
• Atom Count: 3,801 
• Modeled Residue Count: 485 
• Deposited Residue Count: 580 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN VPRBP	A	361	Homo sapiens	Mutation(s): 0  EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4B6 (Homo sapiens) Explore Q9Y4B6  Go to UniProtKB:  Q9Y4B6
PHAROS:  Q9Y4B6 GTEx:  ENSG00000145041

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VPX PROTEIN	B	102	Simian immunodeficiency virus	Mutation(s): 0
UniProt
Find proteins for Q7ZB17 (Simian immunodeficiency virus) Explore Q7ZB17  Go to UniProtKB:  Q7ZB17

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SAM DOMAIN AND HD DOMAIN-CONTAINING PROTEIN	C	117	Mandrillus sphinx	Mutation(s): 0
UniProt
Find proteins for H6WEA4 (Mandrillus sphinx) Explore H6WEA4  Go to UniProtKB:  H6WEA4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.227 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.021	α = 90
b = 102.021	β = 90
c = 265.001	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-22 
Deposition Author(s): Schwefel, D., Boucherit, V.C., Christodoulou, E., Walker, P.A., Stoye, J.P., Bishop, K.N., Taylor, I.A.

Revision History  

• Version 1.0: 2015-04-22
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description