› 7tpp

Electron Microscopy
4.1Å resolution

Cryo-em structure of human prothrombin:prothrombinase at 4.1 Angstrom resolution

Released:
DOI: 10.2210/pdb7tpp/pdb
PDB entry 7tpp coloured by chain, front view.
PDB entry 7tpp coloured by chain, side view.
PDB entry 7tpp coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Cryo-EM structure of the prothrombin-prothrombinase complex.
Ruben EA, Summers B, Rau MJ, Fitzpatrick JAJ, Di Cera E
OpenAccess logo Blood 139 3463-3473 (2022)
PMID: 35427420
Related structures: EMD-26060

Function and Biology Details

Reactions catalysed: 
Selective cleavage of Arg-|-Gly bonds in fibrinogen to form fibrin and release fibrinopeptides A and B.
Selective cleavage of Arg-|-Thr and then Arg-|-Ile bonds in prothrombin to form thrombin.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133138 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Prothrombin Chain: E
Molecule details ›
Chain: E
Length: 579 amino acids
Theoretical weight: 65.37 KDa
Source organism: Homo sapiens
Expression system: Mesocricetus auratus
UniProt:
  • Canonical: P00734 (Residues: 44-622; Coverage: 97%)
Gene name: F2
Sequence domains:
Factor X light chain Chain: A
Molecule details ›
Chain: A
Length: 139 amino acids
Theoretical weight: 15.74 KDa
Source organism: Homo sapiens
Expression system: Mesocricetus auratus
UniProt:
  • Canonical: P00742 (Residues: 41-179; Coverage: 30%)
Gene name: F10
Sequence domains:
Coagulation factor V heavy chain Chain: C
Molecule details ›
Chain: C
Length: 709 amino acids
Theoretical weight: 81.27 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P12259 (Residues: 29-737; Coverage: 32%)
Gene name: F5
Sequence domains: Multicopper oxidase
Coagulation factor V light chain Chain: D
Molecule details ›
Chain: D
Length: 651 amino acids
Theoretical weight: 75.28 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P12259 (Residues: 1574-2224; Coverage: 30%)
Gene name: F5
Sequence domains:
Activated factor Xa heavy chain Chain: B
Molecule details ›
Chain: B
Length: 254 amino acids
Theoretical weight: 28.53 KDa
Source organism: Homo sapiens
Expression system: Mesocricetus auratus
UniProt:
  • Canonical: P00742 (Residues: 235-488; Coverage: 56%)
Gene name: F10
Sequence domains: Trypsin

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.1Å
Relevant EMDB volumes: EMD-26060
Expression system: Mesocricetus auratus

Quick links

Citations

1 review citation

Cryo-EM structures of coagulation factors.
Di Cera et al. (2022)
3 other articles

2 mentions without citation

Cryo-EM structure of the prothrombin-prothrombinase complex.
Ruben et al. (2022)
1 more