[English] 日本語
Yorodumi- EMDB-42405: Preliminary map of the Prothrombin-prothrombinase complex on nano... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42405 | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Preliminary map of the Prothrombin-prothrombinase complex on nano discs | |||||||||||||||||||||||||||
Map data | Unsharpened map | |||||||||||||||||||||||||||
Sample |
| |||||||||||||||||||||||||||
Keywords | Coagulation / Prothrombin / Prothrombinase / nanodisc / complex / BLOOD CLOTTING | |||||||||||||||||||||||||||
Function / homology | Function and homology information response to vitamin K / coagulation factor Xa / platelet alpha granule / Cargo concentration in the ER / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / blood circulation / Extrinsic Pathway of Fibrin Clot Formation / COPII-mediated vesicle transport ...response to vitamin K / coagulation factor Xa / platelet alpha granule / Cargo concentration in the ER / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / blood circulation / Extrinsic Pathway of Fibrin Clot Formation / COPII-mediated vesicle transport / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / COPII-coated ER to Golgi transport vesicle / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of TOR signaling / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of cytosolic calcium ion concentration / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / platelet alpha granule lumen / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / Post-translational protein phosphorylation / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / phospholipid binding / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / extracellular vesicle / Thrombin signalling through proteinase activated receptors (PARs) / Platelet degranulation / heparin binding / positive regulation of cell growth / regulation of cell shape / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of cell migration / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / copper ion binding / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / positive regulation of cell population proliferation / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.47 Å | |||||||||||||||||||||||||||
Authors | Stojanovski BM / Mohammed BM / Di Cera E | |||||||||||||||||||||||||||
Funding support | United States, 8 items
| |||||||||||||||||||||||||||
Citation | Journal: Subcell Biochem / Year: 2024 Title: The Prothrombin-Prothrombinase Interaction. Authors: Bosko M Stojanovski / Bassem M Mohammed / Enrico Di Cera / Abstract: The hemostatic response to vascular injury entails a sequence of proteolytic events where several inactive zymogens of the trypsin family are converted to active proteases. The cascade starts with ...The hemostatic response to vascular injury entails a sequence of proteolytic events where several inactive zymogens of the trypsin family are converted to active proteases. The cascade starts with exposure of tissue factor from the damaged endothelium and culminates with conversion of prothrombin to thrombin in a reaction catalyzed by the prothrombinase complex composed of the enzyme factor Xa, cofactor Va, Ca, and phospholipids. This cofactor-dependent activation is paradigmatic of analogous reactions of the blood coagulation and complement cascades, which makes elucidation of its molecular mechanism of broad significance to the large class of trypsin-like zymogens to which prothrombin belongs. Because of its relevance as the most important reaction in the physiological response to vascular injury, as well as the main trigger of pathological thrombotic complications, the mechanism of prothrombin activation has been studied extensively. However, a molecular interpretation of this mechanism has become available only recently from important developments in structural biology. Here we review current knowledge on the prothrombin-prothrombinase interaction and outline future directions for the study of this key reaction of the coagulation cascade. | |||||||||||||||||||||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_42405.map.gz | 253.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-42405-v30.xml emd-42405.xml | 22.3 KB 22.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42405_fsc.xml | 16.9 KB | Display | FSC data file |
Images | emd_42405.png | 109.7 KB | ||
Masks | emd_42405_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-42405.cif.gz | 5 KB | ||
Others | emd_42405_additional_1.map.gz emd_42405_additional_2.map.gz emd_42405_half_map_1.map.gz emd_42405_half_map_2.map.gz | 474.3 MB 474.3 MB 474.8 MB 474.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42405 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42405 | HTTPS FTP |
-Validation report
Summary document | emd_42405_validation.pdf.gz | 885.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_42405_full_validation.pdf.gz | 884.7 KB | Display | |
Data in XML | emd_42405_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | emd_42405_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42405 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42405 | HTTPS FTP |
-Related structure data
Related structure data | 9cthMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_42405.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unsharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.94 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_42405_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: original half-map A
File | emd_42405_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | original half-map A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: original half-map B
File | emd_42405_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | original half-map B | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map B filtered to resolution (6.5A)
File | emd_42405_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map B filtered to resolution (6.5A) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map A filtered to resolution (6.5A)
File | emd_42405_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map A filtered to resolution (6.5A) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Prothrombin_Prothrombinase complex on lipid nanodiscs.
Entire | Name: Prothrombin_Prothrombinase complex on lipid nanodiscs. |
---|---|
Components |
|
-Supramolecule #1: Prothrombin_Prothrombinase complex on lipid nanodiscs.
Supramolecule | Name: Prothrombin_Prothrombinase complex on lipid nanodiscs. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: The complex is made of coagulation factor Va (derived from human plasma), coagulation factor Xa (Recombinantly expressed in BHK cells) and Prothrombin (Recombinantly expressed in BHK cells). ...Details: The complex is made of coagulation factor Va (derived from human plasma), coagulation factor Xa (Recombinantly expressed in BHK cells) and Prothrombin (Recombinantly expressed in BHK cells). The nanodisc component of the complex is made of the scaffold protein MSP1E3D1 (Recombinantly expressed in bacteria) and the phospholipid component was Porcine Brain phosphatidylserine. |
---|---|
Source (natural) | Organism: Homo sapiens (human) / Tissue: Blood |
-Supramolecule #2: Coagulation Factor Va
Supramolecule | Name: Coagulation Factor Va / type: organelle_or_cellular_component / ID: 2 / Parent: 1 |
---|---|
Source (natural) | Organism: Homo sapiens (human) / Tissue: Blood |
-Supramolecule #3: Coagulation Factor Xa
Supramolecule | Name: Coagulation Factor Xa / type: organelle_or_cellular_component / ID: 3 / Parent: 1 Details: Catalytically inactive full length mutant S379A with C-terminus HPC4 tag. |
---|---|
Source (natural) | Organism: Homo sapiens (human) / Tissue: Blood |
-Supramolecule #4: Prothrombin
Supramolecule | Name: Prothrombin / type: organelle_or_cellular_component / ID: 4 / Parent: 1 Details: Catalytically inactive full length mutant S525A with C-terminus HPC4 tag |
---|---|
Source (natural) | Organism: Homo sapiens (human) / Tissue: Blood |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.01 mg/mL |
---|---|
Buffer | pH: 7.4 / Details: 20 mM HEPES, 150 mM NaCl, and 5 mM CaCl2 |
Grid | Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
Details | Prothrombin:FVa:FXa were mixed in 2:1:2 ratio. 0.01 mg/mL total protein was used for freezing. |
-Electron microscopy
Microscope | TFS GLACIOS |
---|---|
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number real images: 2390 / Average electron dose: 51.28 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
---|---|
Output model | PDB-9cth: |