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Structural basis of thrombin-mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction

X-ray diffraction
2.55Å resolution
PDB entry 3p70 coloured by chain, front view.
PDB entry 3p70 coloured by chain, side view.
PDB entry 3p70 coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero trimer (preferred)
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1
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Assembly Name: Coagulation factor Va complex and Thrombin heavy chain
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Multimeric state: hetero trimer
Accessible surface area: 13726.85 Å2
Buried surface area: 3741.91 Å2
Dissociation area: 299.15 Å2
Dissociation energy (ΔGdiss): -1.03 kcal/mol
Dissociation entropy (TΔSdiss): 6.3 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-133083
Assembly 2
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Assembly Name: Coagulation factor Va complex and Thrombin heavy chain
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Multimeric state: hetero trimer
Accessible surface area: 13376.31 Å2
Buried surface area: 3601.35 Å2
Dissociation area: 307.63 Å2
Dissociation energy (ΔGdiss): -1.36 kcal/mol
Dissociation entropy (TΔSdiss): 5.81 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-133083
Assembly 3
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Assembly Name: Coagulation factor Va complex and Thrombin heavy chain
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Multimeric state: hetero trimer
Accessible surface area: 13733.87 Å2
Buried surface area: 3912.06 Å2
Dissociation area: 299.63 Å2
Dissociation energy (ΔGdiss): -0.37 kcal/mol
Dissociation entropy (TΔSdiss): 5.78 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-133083
Assembly 4 (preferred)
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Assembly Name: Coagulation factor Va complex and Thrombin heavy chain
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Multimeric state: hetero trimer
Accessible surface area: 13615.83 Å2
Buried surface area: 4174.14 Å2
Dissociation area: 308.99 Å2
Dissociation energy (ΔGdiss): -1.38 kcal/mol
Dissociation entropy (TΔSdiss): 5.97 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-133083

Macromolecules

Thrombin light chain
Chains: A, C, E, G
Length: 36 amino acids
Theoretical weight: 4.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 328-363; Coverage: 6%)
Gene name: F2
Pfam: Thrombin light chain
InterPro:
Thrombin light chain in PDB entry 3p70, assembly 4, front view.
Thrombin light chain in PDB entry 3p70, assembly 4, side view.
Thrombin light chain in PDB entry 3p70, assembly 4, top view.
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Thrombin heavy chain
Chains: B, D, F, H
Length: 259 amino acids
Theoretical weight: 29.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Pfam: Trypsin
InterPro:
CATH: Trypsin-like serine proteases
Thrombin heavy chain in PDB entry 3p70, assembly 4, front view.
Thrombin heavy chain in PDB entry 3p70, assembly 4, side view.
Thrombin heavy chain in PDB entry 3p70, assembly 4, top view.
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Coagulation factor V heavy chain
Chains: M, N, O, P
Length: 71 amino acids
Theoretical weight: 8.39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P12259 (Residues: 685-737; Coverage: 2%)
Gene name: F5
InterPro: Nucleotidyltransferase superfamily
Coagulation factor V heavy chain in PDB entry 3p70, assembly 4, front view.
Coagulation factor V heavy chain in PDB entry 3p70, assembly 4, side view.
Coagulation factor V heavy chain in PDB entry 3p70, assembly 4, top view.
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