- EMDB-41400: Structural architecture of the acidic region of the B domain of c... -
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Basic information
Entry
Database: EMDB / ID: EMD-41400
Title
Structural architecture of the acidic region of the B domain of coagulation factor V
Map data
Consensus map plasma factor V
Sample
Tissue: Coagulation plasma Factor V
Protein or peptide: Coagulation Plasma Factor V
Keywords
Coagulation / Pro-cofactor / Factor V / B Domain / Acidic Region / 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, HL139554 and HL147821
United States
Childrens Discovery Institute of Washington University and St. Louis Childrens Hospital
CDI-CORE-2015-505 and CDI-CORE-2019-813
United States
The Foundation for Barnes-Jewish Hospital
3770
United States
Washington University Diabetes Research Center
DK020579
United States
National Institutes of Health/National Cancer Institute (NIH/NCI)
P30 CA091842
United States
Citation
Journal: J Thromb Haemost / Year: 2024 Title: Structural architecture of the acidic region of the B domain of coagulation factor V. Authors: Bassem M Mohammed / Katherine Basore / Brock Summers / Leslie A Pelc / Enrico Di Cera / Abstract: BACKGROUND: Coagulation factor (F)V features an A1-A2-B-A3-C1-C2 domain organization and functions as the inactive precursor of FVa, a component of the prothrombinase complex required for rapid ...BACKGROUND: Coagulation factor (F)V features an A1-A2-B-A3-C1-C2 domain organization and functions as the inactive precursor of FVa, a component of the prothrombinase complex required for rapid thrombin generation in the penultimate step of the coagulation cascade. An intramolecular interaction within the large B domain (residues 710-1545) involves the basic region (BR, residues 963-1008) and acidic region (AR, residues 1493-1537) and locks FV in its inactive state. However, structural information on this important regulatory interaction or on the separate architecture of the AR and BR remains elusive due to conformational disorder of the B domain. OBJECTIVES: To reveal the structure of the BR-AR interaction or of its separate components. METHODS: The structure of FV is solved by cryogenic electron microscopy. RESULTS: A new 3.05 Å resolution cryogenic electron microscopy structure of FV confirms the overall organization of the A and C domains but resolves the segment 1507 to 1545 within a largely ...RESULTS: A new 3.05 Å resolution cryogenic electron microscopy structure of FV confirms the overall organization of the A and C domains but resolves the segment 1507 to 1545 within a largely disordered B domain. The segment contains most of the AR and is organized as recently reported in FV short, a spliced variant of FV with a significantly shorter and less disordered B domain. CONCLUSION: The similar architecture of the AR in FV and FV short provides structural context for physiologically important interactions of this region with the BR in FV and with the basic C-terminal ...CONCLUSION: The similar architecture of the AR in FV and FV short provides structural context for physiologically important interactions of this region with the BR in FV and with the basic C-terminal end of tissue factor pathway inhibitor α in FV short.
pH: 7.4 / Details: 20 mM HEPES, 150 mM NaCl, 5 mM CaCl2
Grid
Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.009300000000000001 kPa
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
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Electron microscopy
Microscope
FEI TITAN
Specialist optics
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recording
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 2 / Number real images: 8429 / Average exposure time: 1.65 sec. / Average electron dose: 66.0 e/Å2 Details: 2 Grids imaged one at 0.1 mg/mL and the second at 0.2 mg/mL using the same acquisition parameters.
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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