+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29011 | ||||||||||||
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Title | Cryo-EM structure of coagulation factor V short | ||||||||||||
Map data | composite map used for model building | ||||||||||||
Sample |
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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) / blood coagulation / extracellular vesicle / Platelet degranulation / signaling receptor activity / copper ion binding / endoplasmic reticulum lumen / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Mohammed BM / Pelc LA / Rau MJ / Di Cera E | ||||||||||||
Funding support | United States, 3 items
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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. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29011.map.gz | 125.4 MB | EMDB map data format | |
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Header (meta data) | emd-29011-v30.xml emd-29011.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
Images | emd_29011.png | 115.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29011 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29011 | HTTPS FTP |
-Validation report
Summary document | emd_29011_validation.pdf.gz | 449.8 KB | Display | EMDB validaton report |
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Full document | emd_29011_full_validation.pdf.gz | 449.4 KB | Display | |
Data in XML | emd_29011_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | emd_29011_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29011 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29011 | HTTPS FTP |
-Related structure data
Related structure data | 8fdgMC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29011.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | composite map used for model building | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.9 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Recombinantly expressed coagulation factor V short full length wi...
Entire | Name: Recombinantly expressed coagulation factor V short full length with a c-terminus HPC4 tag |
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Components |
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-Supramolecule #1: Recombinantly expressed coagulation factor V short full length wi...
Supramolecule | Name: Recombinantly expressed coagulation factor V short full length with a c-terminus HPC4 tag type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) / Organ: Liver / Tissue: Blood |
-Macromolecule #1: Coagulation factor V
Macromolecule | Name: Coagulation factor V / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) / Organ: Liver / Tissue: Blood |
Molecular weight | Theoretical: 172.748234 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AQLRQFYVAA QGISWSYRPE PTNSSLNLSV TSFKKIVYRE YEPYFKKEKP QSTISGLLGP TLYAEVGDII KVHFKNKADK PLSIHPQGI RYSKLSEGAS YLDHTFPAEK MDDAVAPGRE YTYEWSISED SGPTHDDPPC LTHIYYSHEN LIEDFNSGLI G PLLICKKG ...String: AQLRQFYVAA QGISWSYRPE PTNSSLNLSV TSFKKIVYRE YEPYFKKEKP QSTISGLLGP TLYAEVGDII KVHFKNKADK PLSIHPQGI RYSKLSEGAS YLDHTFPAEK MDDAVAPGRE YTYEWSISED SGPTHDDPPC LTHIYYSHEN LIEDFNSGLI G PLLICKKG TLTEGGTQKT FDKQIVLLFA VFDESKSWSQ SSSLMYTVNG YVNGTMPDIT VCAHDHISWH LLGMSSGPEL FS IHFNGQV LEQNHHKVSA ITLVSATSTT ANMTVGPEGK WIISSLTPKH LQAGMQAYID IKNCPKKTRN LKKITREQRR HMK RWEYFI AAEEVIWDYA PVIPANMDKK YRSQHLDNFS NQIGKHYKKV MYTQYEDESF TKHTVNPNMK EDGILGPIIR AQVR DTLKI VFKNMASRPY SIYPHGVTFS PYEDEVNSSF TSGRNNTMIR AVQPGETYTY KWNILEFDEP TENDAQCLTR PYYSD VDIM RDIASGLIGL LLICKSRSLD RRGIQRAADI EQQAVFAVFD ENKSWYLEDN INKFCENPDE VKRDDPKFYE SNIMST ING YVPESITTLG FCFDDTVQWH FCSVGTQNEI LTIHFTGHSF IYGKRHEDTL TLFPMRGESV TVTMDNVGTW MLTSMNS SP RSKKLRLKFR DVKCIPDDDE DSYEIFEPPE STVMATRKMH DRLEPEDEES DADYDYQNRL AAALGIRSFR NSSLNQEE E EFNLTALALE NGTEFVSSNT DIIVGSNYSS PSNILGQMPS PSSPTLNDTF LSKEFNPLVI VGLSKDGTDY IEIIPKEEV QSSEDDYAEI DYVPYDDPYK TDVRTNINSS RDPDNIAAWY LRSNNGNRRN YYIAAEEISW DYSEFVQRET DIEDSDDIPE DTTYKKVVF RKYLDSTFTK RDPRGEYEEH LGILGPIIRA EVDDVIQVRF KNLASRPYSL HAHGLSYEKS SEGKTYEDDS P EWFKEDNA VQPNSSYTYV WHATERSGPE SPGSACRAWA YYSAVNPEKD IHSGLIGPLL ICQKGILHKD SNMPVDMREF VL LFMTFDE KKSWYYEKKS RSSWRLTSSE MKKSHEFHAI NGMIYSLPGL KMYEQEWVRL HLLNIGGSQD IHVVHFHGQT LLE NGNKQH QLGVWPLLPG SFKTLEMKAS KPGWWLLNTE VGENQRAGMQ TPFLIMDRDC RMPMGLSTGI ISDSQIKASE FLGY WEPRL ARLNNGGSYN AWSVEKLAAE FASKPWIQVD MQKEVIITGI QTQGAKHYLK SCYTTEFYVA YSSNQINWQI FKGNS TRNV MYFNGNSDAS TIKENQFDPP IVARYIRISP TRAYNRPTLR LELQGCEVNG CSTPLGMENG KIENKQITAS SFKKSW WGD YWEPFRARLN AQGRVNAWQA KANNNKQWLE IDLLKIKKIT AIITQGCKSL SSEMYVKSYT IHYSEQGVEW KPYRLKS SM VDKIFEGNTN TKGHVKNFFN PPIISRFIRV IPKTWNQSIA LRLELFGCDI YEDQVDPRLI DGK UniProtKB: Coagulation factor V, Coagulation factor V |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Details: 2 second blot 20 second wait time. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: Cs corrector |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-46 / Number grids imaged: 1 / Number real images: 3316 / Average exposure time: 9.36 sec. / Average electron dose: 55.09 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. V4.0.3) / Number images used: 147000 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-8fdg: |