Experimental Data Snapshot
(2013) J Mol Biology 425: 1961-1981
Crystal structures of factor (F) VIIa/soluble tissue factor (TF), obtained under high Mg(2+) (50mM Mg(2+)/5mM Ca(2+)), have three of seven Ca(2+) sites in the γ-carboxyglutamic acid (Gla) domain replaced by Mg(2+) at positions 1, 4, and 7. We now report structures under low Mg(2+) (2.5mM Mg(2+)/5mM Ca(2+)) as well as under high Ca(2+) (5mM Mg(2+)/45 mM Ca(2+)). Under low Mg(2+), four Ca(2+) and three Mg(2+) occupy the same positions as in high-Mg(2+) structures. Conversely, under low Mg(2+), reexamination of the structure of Gla domain of activated Protein C (APC) complexed with soluble endothelial Protein C receptor (sEPCR) has position 4 occupied by Ca(2+) and positions 1 and 7 by Mg(2+). Nonetheless, in direct binding experiments, Mg(2+) replaced three Ca(2+) sites in the unliganded Protein C or APC. Further, the high-Ca(2+) condition was necessary to replace Mg4 in the FVIIa/soluble TF structure. In biological studies, Mg(2+) enhanced phospholipid binding to FVIIa and APC at physiological Ca(2+). Additionally, Mg(2+) potentiated phospholipid-dependent activations of FIX and FX by FVIIa/TF and inactivation of activated factor V by APC. Since APC and FVIIa bind to sEPCR involving similar interactions, we conclude that under the low-Mg(2+) condition, sEPCR binding to APC-Gla (or FVIIa-Gla) replaces Mg4 by Ca4 with an attendant conformational change in the Gla domain ω-loop. Moreover, since phospholipid and sEPCR bind to FVIIa or APC via the ω-loop, we predict that phospholipid binding also induces the functional Ca4 conformation in this loop. Cumulatively, the data illustrate that Mg(2+) and Ca(2+) act in concert to promote coagulation and anticoagulation.
 Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (PTY)
Biological assembly 1 assigned by authors and generated by PISA (software)
 Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (PTY)
Biological assembly 2 assigned by authors and generated by PISA (software)
Macromolecule Content 
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Endothelial protein C receptor | 193 | Homo sapiens | Mutation(s): 0  | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9UNN8 (Homo sapiens) Explore Q9UNN8  Go to UniProtKB:  Q9UNN8 | |||||
PHAROS:  Q9UNN8 GTEx:  ENSG00000101000  | |||||
Entity Groups  | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9UNN8 | ||||
Glycosylation | |||||
| Glycosylation Sites: 3 | Go to GlyGen: Q9UNN8-1 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Vitamin K-dependent protein C | 33 | Homo sapiens | Mutation(s): 0  EC: 3.4.21.69 | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P04070 (Homo sapiens) Explore P04070  Go to UniProtKB:  P04070 | |||||
PHAROS:  P04070 GTEx:  ENSG00000115718  | |||||
Entity Groups  | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P04070 | ||||
Sequence AnnotationsExpand | |||||
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| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| CGU Query on CGU | C, D | L-PEPTIDE LINKING | C6 H9 N O6 | GLU | |
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 59.22 | α = 90 |
| b = 62.36 | β = 101.81 |
| c = 71.03 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.