› 5aja

X-ray diffraction
2.65Å resolution

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

Released:
DOI: 10.2210/pdb5aja/pdb
PDB entry 5aja coloured by chain, front view.
PDB entry 5aja coloured by chain, side view.
PDB entry 5aja coloured by chain, top view.
Source organisms:
Primary publication:
Molecular determinants for recognition of divergent SAMHD1 proteins by the lentiviral accessory protein Vpx.
Schwefel D, Boucherit VC, Christodoulou E, Walker PA, Stoye JP, Bishop KN, Taylor IA
Cell Host Microbe 17 489-99 (2015)
PMID: 25856754

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-124851 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
DDB1- and CUL4-associated factor 1 Chain: A
Molecule details ›
Chain: A
Length: 361 amino acids
Theoretical weight: 41.07 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9Y4B6 (Residues: 1058-1396; Coverage: 23%)
Gene names: DCAF1, KIAA0800, RIP, VPRBP
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase
Protein Vpr Chain: B
Molecule details ›
Chain: B
Length: 102 amino acids
Theoretical weight: 11.94 KDa
Source organism: Simian immunodeficiency virus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q7ZB17 (Residues: 1-99; Coverage: 100%)
Gene names: vpr, vpx
Sequence domains: VPR/VPX protein
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 Chain: C
Molecule details ›
Chain: C
Length: 117 amino acids
Theoretical weight: 12.91 KDa
Source organism: Mandrillus sphinx
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: H6WEA4 (Residues: 1-114; Coverage: 18%)
Gene name: SAMHD1
Sequence domains: SAM domain (Sterile alpha motif)

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P6522
Unit cell:
a: 102.021Å b: 102.021Å c: 265.001Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.176 0.174 0.227
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Interplay between the virus and the ubiquitin-proteasome system: molecular mechanism of viral pathogenesis.
Luo H. (2016)
4 more

8 mentions without citation

HIV suppression by host restriction factors and viral immune evasion.
Jia et al. (2015)
7 more