4cc9

X-ray diffraction
2.47Å resolution

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)

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-148620 (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 Vpx Chain: B
Molecule details ›
Chain: B
Length: 119 amino acids
Theoretical weight: 13.59 KDa
Source organism: Simian immunodeficiency virus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P19508 (Residues: 1-112; Coverage: 100%)
Gene name: 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: 71 amino acids
Theoretical weight: 8.05 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9Y3Z3 (Residues: 582-626; Coverage: 7%)
Gene names: MOP5, SAMHD1

Ligands and Environments

2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P212121
Unit cell:
a: 74.25Å b: 82.881Å c: 115.561Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.176 0.216
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli BL21(DE3)