› 9bvm

Electron Microscopy
3.4Å resolution

Vitamin K-dependent gamma-carboxylase with protein C propeptide and glutamate-rich region and with vitamin K hydroquinone

Released:
DOI: 10.2210/pdb9bvm/pdb
PDB entry 9bvm coloured by chain, front view.
PDB entry 9bvm coloured by chain, side view.
PDB entry 9bvm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis of vitamin K driven γ-carboxylation at membrane interface.
Cao Q, Ammerman A, Saimi M, Lin Z, Shen G, Chen H, Sun J, Chai M, Liu S, Hsu FF, Krezel AM, Gross ML, Xu J, Garcia BA, Liu B, Li W
Nature (2025)
PMID: 39880037
Related structures: EMD-44937

Function and Biology Details

Reactions catalysed: 
[Peptidyl]-4-carboxyglutamate + 2,3-epoxyphylloquinone + H(2)O = [peptidyl]-glutamate + CO(2) + O(2) + phylloquinol
Degradation of blood coagulation factors Va and VIIIa.
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-284194 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Vitamin K-dependent gamma-carboxylase Chain: A
Molecule details ›
Chain: A
Length: 732 amino acids
Theoretical weight: 85.01 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P38435 (Residues: 27-758; Coverage: 97%)
Gene names: GC, GGCX
Sequence domains:
Vitamin K-dependent protein C light chain Chain: P
Molecule details ›
Chain: P
Length: 70 amino acids
Theoretical weight: 8.22 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P04070 (Residues: 19-88; Coverage: 16%)
Gene name: PROC
Sequence domains: Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
3 bound ligands:
Ligand A1AVC 1 x A1AVC
Ligand 6PL 2 x 6PL
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.4Å
Relevant EMDB volumes: EMD-44937
Expression system: Homo sapiens

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