8fdg

Cryo-EM structure of coagulation factor V short

Method: ELECTRON MICROSCOPY Dmax: 129.3 Å Quality: GOOD

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

Coagulation factor V

Homo sapiens

UniProt P12259

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 29–783 Chain A; UniProt 1487–2224 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE;2 second blot 20 second wait time Resolution 3.20 Å

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.

16 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FA5_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–755; UniProt 29–783 Author chain A; PDBConstruct 756–1493; UniProt 1487–2224

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 8fdg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8fdg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8fdg
Deposition date deposition_date2022-12-03
Structure title titleCryo-EM structure of coagulation factor V short
Keywords keywordsBLOOD CLOTTING; BLOOD CLOTTING
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier38.93
Radius of gyration Rg (electron density) rg_electron38.44
Forward intensity I(0) i0457875000.00
Molecular weight molecular_weight172500.0 kDa
Excluded volume excluded_volume215010 ų
Envelope volume envelope_volume299660 ų
Hydration-shell volume shell_volume64302 ų
Envelope diameter envelope_diameter133.0
Shell Rg shell_rg44.93
Envelope Rg envelope_rg38.16
Shape Rg shape_rg38.44
Total Rg total_rg38.81
Total atoms total_atoms12163
Residues n_residues1505
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 dmax129.3
Rg (real space) rg_real38.90
Rg uncertainty (real space) rg_real_error0.70
I(0) (real space) i0_real4.5790e+08
I(0) uncertainty (real space) i0_real_error6.2620e+06
Rg (reciprocal space) rg_reciprocal38.92
I(0) (reciprocal space) i0_reciprocal457900000.0000
Solution quality estimate total_estimate0.8729
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.3
Skewness Skewness skewness0.378
Kurtosis Kurtosis kurtosis-0.223
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha95790000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.846

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id8fdgA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id8fdgA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like

8. Citations (1)

9. Files and Curves (10)