- PDB-8fdg: Cryo-EM structure of coagulation factor V short -
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Basic information
Entry
Database: PDB / ID: 8fdg
Title
Cryo-EM structure of coagulation factor V short
Components
Coagulation factor V
Keywords
BLOOD CLOTTING
Function / homology
Function and homology information
response to vitamin K / platelet alpha granule / Cargo concentration in the ER / blood circulation / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / Common Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / Post-translational protein phosphorylation ...response to vitamin K / platelet alpha granule / Cargo concentration in the ER / blood circulation / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / Common Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / extracellular vesicle / blood coagulation / Platelet degranulation / signaling receptor activity / copper ion binding / endoplasmic reticulum lumen / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function
Coagulation factor 5/8-like / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Multicopper oxidase, N-terminal ...Coagulation factor 5/8-like / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin / Galactose-binding-like domain superfamily Similarity search - Domain/homology
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)
HL049413
United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)
HL139554
United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)
HL147821
United States
Citation
Journal: Blood / Year: 2023 Title: Cryo-EM structure of coagulation factor V short. Authors: Bassem M Mohammed / Leslie A Pelc / Michael J Rau / Enrico Di Cera / Abstract: Coagulation factor V (fV) is the precursor of activated fV (fVa), an essential component of the prothrombinase complex required for the rapid activation of prothrombin in the penultimate step of the ...Coagulation factor V (fV) is the precursor of activated fV (fVa), an essential component of the prothrombinase complex required for the rapid activation of prothrombin in the penultimate step of the coagulation cascade. In addition, fV regulates the tissue factor pathway inhibitor α (TFPIα) and protein C pathways that inhibit the coagulation response. A recent cryogenic electron microscopy (cryo-EM) structure of fV has revealed the architecture of its A1-A2-B-A3-C1-C2 assembly but left the mechanism that keeps fV in its inactive state unresolved because of an intrinsic disorder in the B domain. A splice variant of fV, fV short, carries a large deletion of the B domain that produces constitutive fVa-like activity and unmasks epitopes for the binding of TFPIα. The cryo-EM structure of fV short was solved at 3.2 Å resolution and revealed the arrangement of the entire A1-A2-B-A3-C1-C2 assembly. The shorter B domain stretches across the entire width of the protein, making contacts with the A1, A2, and A3 domains but suspended over the C1 and C2 domains. In the portion distal to the splice site, several hydrophobic clusters and acidic residues provide a potential binding site for the basic C-terminal end of TFPIα. In fV, these epitopes may bind intramolecularly to the basic region of the B domain. The cryo-EM structure reported in this study advances our understanding of the mechanism that keeps fV in its inactive state, provides new targets for mutagenesis and facilitates future structural analysis of fV short in complex with TFPIα, protein S, and fXa.
Average exposure time: 9.36 sec. / Electron dose: 55.09 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3316
EM imaging optics
Spherical aberration corrector: Cs corrector
Image scans
Width: 4096 / Height: 4096 / Movie frames/image: 46 / Used frames/image: 1-46
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Processing
Software
Name
Version
Classification
phenix.real_space_refine
1.20.1_4487
refinement
PHENIX
1.20.1_4487
refinement
EM software
ID
Name
Version
Category
Details
2
EPU
2.12.1.2782
imageacquisition
7
Coot
0.9.6
modelfitting
12
cryoSPARC
V4.0.3
3Dreconstruction
13
PHENIX
1.20.1
modelrefinement
phenix.real_space_refine
CTF correction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Symmetry
Point symmetry: C1 (asymmetric)
3D reconstruction
Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 147000 / Symmetry type: POINT
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