9tjx

Structure of factor VII Gla domain bound to EPCR

Method: X-RAY DIFFRACTION Dmax: 131.8 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Endothelial protein C receptor

Homo sapiens

UniProt Q9UNN8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 18–210 Not recorded Factor VII light chain × 1 (P08709) ;alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 SO4 SULFATE ION × 2 PTY PHOSPHATIDYLETHANOLAMINE × 1 CA CALCIUM ION × 5 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;295 K;0.2 M Ammonium sulfate, 0.1 M Tris PH 8.5, 12 % w/v PEG 8000 Resolution 3.00 Å R-free 0.295
2 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 18–210 Not recorded Factor VII light chain × 1 (P08709) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 2 PTY PHOSPHATIDYLETHANOLAMINE × 1 CA CALCIUM ION × 5 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;295 K;0.2 M Ammonium sulfate, 0.1 M Tris PH 8.5, 12 % w/v PEG 8000 Resolution 3.00 Å R-free 0.295
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 18–210 Not recorded Factor VII light chain × 1 (P08709) PTY PHOSPHATIDYLETHANOLAMINE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 5 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;295 K;0.2 M Ammonium sulfate, 0.1 M Tris PH 8.5, 12 % w/v PEG 8000 Resolution 3.00 Å R-free 0.295
4 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 18–210 Not recorded Factor VII light chain × 1 (P08709) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1 PTY PHOSPHATIDYLETHANOLAMINE × 1 CA CALCIUM ION × 5 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;295 K;0.2 M Ammonium sulfate, 0.1 M Tris PH 8.5, 12 % w/v PEG 8000 Resolution 3.00 Å R-free 0.295

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

12 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EPCR_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–195; UniProt 18–210 Author chain B; PDBConstruct 3–195; UniProt 18–210 Author chain C; PDBConstruct 3–195; UniProt 18–210 Author chain D; PDBConstruct 3–195; UniProt 18–210

Factor VII light chain

OrganismNot specified

UniProt P08709

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 61–92 Non-standard monomer:Yes (specific site not provided by mmCIF) Endothelial protein C receptor × 1 (Q9UNN8) ;alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 SO4 SULFATE ION × 2 PTY PHOSPHATIDYLETHANOLAMINE × 1 CA CALCIUM ION × 5 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;295 K;0.2 M Ammonium sulfate, 0.1 M Tris PH 8.5, 12 % w/v PEG 8000 Resolution 3.00 Å R-free 0.295
2 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain L; UniProt 61–92 Non-standard monomer:Yes (specific site not provided by mmCIF) Endothelial protein C receptor × 1 (Q9UNN8) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 2 PTY PHOSPHATIDYLETHANOLAMINE × 1 CA CALCIUM ION × 5 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;295 K;0.2 M Ammonium sulfate, 0.1 M Tris PH 8.5, 12 % w/v PEG 8000 Resolution 3.00 Å R-free 0.295
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain R; UniProt 61–92 Non-standard monomer:Yes (specific site not provided by mmCIF) Endothelial protein C receptor × 1 (Q9UNN8) PTY PHOSPHATIDYLETHANOLAMINE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 5 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;295 K;0.2 M Ammonium sulfate, 0.1 M Tris PH 8.5, 12 % w/v PEG 8000 Resolution 3.00 Å R-free 0.295
4 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 61–92 Non-standard monomer:Yes (specific site not provided by mmCIF) Endothelial protein C receptor × 1 (Q9UNN8) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1 PTY PHOSPHATIDYLETHANOLAMINE × 1 CA CALCIUM ION × 5 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;295 K;0.2 M Ammonium sulfate, 0.1 M Tris PH 8.5, 12 % w/v PEG 8000 Resolution 3.00 Å R-free 0.295

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

113 other PDB entries and 120 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FA7_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain E; PDBConstruct 1–32; UniProt 61–92 Author chain F; PDBConstruct 1–32; UniProt 61–92 Author chain L; PDBConstruct 1–32; UniProt 61–92 Author chain R; PDBConstruct 1–32; UniProt 61–92

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9tjx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9tjx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9tjx
Deposition date deposition_date2025-12-08
Structure title titleStructure of factor VII Gla domain bound to EPCR
Keywords keywordsFactor VII, activated factor VII, EPCR, GLA DOMAIN, COMPLEX, CALCIUM IONS, BLOOD CLOTTING; BLOOD CLOTTING
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier39.67
Radius of gyration Rg (electron density) rg_electron39.25
Forward intensity I(0) i0143531000.00
Molecular weight molecular_weight96505.0 kDa
Excluded volume excluded_volume120220 ų
Envelope volume envelope_volume169560 ų
Hydration-shell volume shell_volume37202 ų
Envelope diameter envelope_diameter127.1
Shell Rg shell_rg43.21
Envelope Rg envelope_rg38.60
Shape Rg shape_rg39.19
Total Rg total_rg39.72
Total atoms total_atoms6756
Residues n_residues755
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax131.8
Rg (real space) rg_real39.96
Rg uncertainty (real space) rg_real_error1.24
I(0) (real space) i0_real1.4350e+08
I(0) uncertainty (real space) i0_real_error2.4550e+06
Rg (reciprocal space) rg_reciprocal39.79
I(0) (reciprocal space) i0_reciprocal143500000.0000
Solution quality estimate total_estimate0.7940
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.2
Skewness Skewness skewness0.354
Kurtosis Kurtosis kurtosis-0.713
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11760000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.815; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (12)

8. Citations (1)

9. Files and Curves (10)