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- EMDB-73327: Composite map of the meizothrombinDESF1, factor Xa and factor Va ... -

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Basic information

Entry
Database: EMDB / ID: EMD-73327
TitleComposite map of the meizothrombinDESF1, factor Xa and factor Va complex
Map dataComposite map of the meizothrombinDESF1,factor Xa, factor Va complex
Sample
  • Complex: Complex of meizothrombinDESF1, factor Xa and factor Va
    • Complex: Coagulation factor X domains and Thrombin chains
      • Protein or peptide: Coagulation factor X
      • Protein or peptide: Meizothrombin
      • Protein or peptide: Thrombin heavy chain
    • Complex: Coagulation factor V light and heavy chains
      • Protein or peptide: Coagulation factor Va light chain
      • Protein or peptide: Coagulation factor V heavy chain
KeywordsCoagulation cascade / Serine Proteases / Thrombotic / Clotting Factors / 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 / COPII-coated ER to Golgi transport vesicle / : / 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 / COPII-coated ER to Golgi transport vesicle / : / COPII-mediated vesicle transport / : / thrombospondin receptor activity / blood circulation / thrombin / thrombin-activated receptor signaling pathway / Defective factor XII causes hereditary angioedema / negative regulation of astrocyte differentiation / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / ligand-gated ion channel signaling pathway / positive regulation of collagen biosynthetic process / negative regulation of platelet activation / negative regulation of blood coagulation / negative regulation of fibrinolysis / blood coagulation, fibrin clot formation / positive regulation of blood coagulation / positive regulation of TOR signaling / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / : / Gamma-carboxylation of protein precursors / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of cytosolic calcium ion concentration / fibrinolysis / : / negative regulation of proteolysis / endoplasmic reticulum-Golgi intermediate compartment membrane / negative regulation of cytokine production involved in inflammatory response / platelet alpha granule lumen / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / growth factor activity / positive regulation of receptor signaling pathway via JAK-STAT / Post-translational protein phosphorylation / lipopolysaccharide binding / platelet activation / phospholipid binding / positive regulation of protein localization to nucleus / response to wounding / 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 / blood coagulation / positive regulation of insulin secretion / Platelet degranulation / regulation of cell shape / antimicrobial humoral immune response mediated by antimicrobial peptide / heparin binding / extracellular vesicle / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of cell growth / blood microparticle / G alpha (q) signalling events / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / endoplasmic reticulum lumen / receptor ligand activity / copper ion binding / serine-type endopeptidase activity / signaling receptor binding / external side of plasma membrane / calcium ion binding / positive regulation of cell population proliferation / proteolysis / : / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Coagulation factor 5/8-like / : / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Coagulation factors 5/8 type C domain (FA58C) signature 2. / 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. / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : ...Coagulation factor 5/8-like / : / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Coagulation factors 5/8 type C domain (FA58C) signature 2. / 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. / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / F5/8 type C domain / Coagulation factor-like, Gla domain superfamily / Coagulation factor 5/8 C-terminal domain / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Multicopper oxidase, N-terminal / Multicopper oxidase / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Kringle domain / Calcium-binding EGF-like domain signature. / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Aspartic acid and asparagine hydroxylation site. / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / Cupredoxin / EGF-like domain signature 2. / EGF-like domain / Galactose-binding-like domain superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Prothrombin / Coagulation factor X / Coagulation factor V
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.84 Å
AuthorsStojanovski BM / Mohammed BM / Basore K / Di Cera E
Funding support United States, 5 items
OrganizationGrant numberCountry
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
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)P30DK020579 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA091842 United States
CitationJournal: Blood / Year: 2026
Title: Molecular mechanism of cleavage at R271 during prothrombin activation revealed by cryo-EM.
Authors: Bosko Stojanovski / Bassem M Mohammed / Katherine Basore / Enrico Di Cera /
Abstract: The conversion of the inactive zymogen prothrombin to the active protease thrombin in the common pathway of the coagulation cascade is the molecular event responsible for the pathophysiology of ...The conversion of the inactive zymogen prothrombin to the active protease thrombin in the common pathway of the coagulation cascade is the molecular event responsible for the pathophysiology of hemostasis and thrombosis. The conversion entails two proteolytic cleavages at R320 and R271 by the prothrombinase complex composed of the enzyme factor Xa (fXa), the cofactor fVa, Ca2+ and phospholipids. A recent cryogenic electron microscopy (cryo-EM) structure revealed how cleavage at R320 generates the active intermediate meizothrombin in the first step of the activation pathway. Here we present the 3.8 Å resolution cryo-EM structure of a truncated form of meizothrombin (mzTDF1) bound to fVa and fXa that reveals how the second cleavage at R271 generates thrombin. The cleavage is brokered by molecular contacts that involve mostly the protease domains of mzTDF1 and fXa and largely validate the results from biochemical studies. The switch in cleavage site from R320 to R271 involves a significant reorientation rather than conformational transitions of the protease domain of mzTDF1 that moves the guanidinium group of R271 more than 20 Å into the primary specificity pocket of fXa. The findings complete the cryo-EM structural analysis of prothrombin activation along the meizothrombin pathway and advance our molecular understanding of a reaction critical to the pathophysiology of blood coagulation.
History
DepositionOct 15, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73327.png

Downloads & links

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Map

FileDownload / File: emd_73327.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of the meizothrombinDESF1,factor Xa, factor Va complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 400 pix.
= 336.8 Å		0.84 Å/pix.
x 400 pix.
= 336.8 Å		0.84 Å/pix.
x 400 pix.
= 336.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.842 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.9
Minimum - Maximum-0.048418988 - 82.597909999999999
Average (Standard dev.)0.015908005 (±1.1596515)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 336.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Complex of meizothrombinDESF1, factor Xa and factor Va

EntireName: Complex of meizothrombinDESF1, factor Xa and factor Va
Components
  • Complex: Complex of meizothrombinDESF1, factor Xa and factor Va
    • Complex: Coagulation factor X domains and Thrombin chains
      • Protein or peptide: Coagulation factor X
      • Protein or peptide: Meizothrombin
      • Protein or peptide: Thrombin heavy chain
    • Complex: Coagulation factor V light and heavy chains
      • Protein or peptide: Coagulation factor Va light chain
      • Protein or peptide: Coagulation factor V heavy chain

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Supramolecule #1: Complex of meizothrombinDESF1, factor Xa and factor Va

SupramoleculeName: Complex of meizothrombinDESF1, factor Xa and factor Va
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Coagulation factor X domains and Thrombin chains

SupramoleculeName: Coagulation factor X domains and Thrombin chains / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Coagulation factor V light and heavy chains

SupramoleculeName: Coagulation factor V light and heavy chains / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2, #5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Coagulation factor X

MacromoleculeName: Coagulation factor X / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: coagulation factor Xa
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.58934 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: FTRKLCSLDN GDCDQFCHEE QNSVVCSCAR GYTLADNGKA CIPTGPYPCG KQTLERRKRS VAQATSSSGE APDSITWKPY DAADLDPTE NPFDLLDFNQ TQPERGDNNL TRIVGGQECK DGECPWQALL INEENEGFCG GTILSEFYIL TAAHCLYQAK R FKVRVGDR ...String:
FTRKLCSLDN GDCDQFCHEE QNSVVCSCAR GYTLADNGKA CIPTGPYPCG KQTLERRKRS VAQATSSSGE APDSITWKPY DAADLDPTE NPFDLLDFNQ TQPERGDNNL TRIVGGQECK DGECPWQALL INEENEGFCG GTILSEFYIL TAAHCLYQAK R FKVRVGDR NTEQEEGGEA VHEVEVVIKH NRFTKETYDF DIAVLRLKTP ITFRMNVAPA CLPERDWAES TLMTQKTGIV SG FGRTHEK GRQSTRLKML EVPYVDRNSC KLSSSFIITQ NMFCAGYDTK QEDACQGDAG GPHVTRFKDT YFVTGIVSWG EGC ARKGKY GIYTKVTAFL KWIDRSMK

UniProtKB: Coagulation factor X

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Macromolecule #2: Coagulation factor Va light chain

MacromoleculeName: Coagulation factor Va light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.283008 KDa
SequenceString: SNNGNRRNYY IAAEEISWDY SEFVQRETDI EDSDDIPEDT TYKKVVFRKY LDSTFTKRDP RGEYEEHLGI LGPIIRAEVD DVIQVRFKN LASRPYSLHA HGLSYEKSSE GKTYEDDSPE WFKEDNAVQP NSSYTYVWHA TERSGPESPG SACRAWAYYS A VNPEKDIH ...String:
SNNGNRRNYY IAAEEISWDY SEFVQRETDI EDSDDIPEDT TYKKVVFRKY LDSTFTKRDP RGEYEEHLGI LGPIIRAEVD DVIQVRFKN LASRPYSLHA HGLSYEKSSE GKTYEDDSPE WFKEDNAVQP NSSYTYVWHA TERSGPESPG SACRAWAYYS A VNPEKDIH SGLIGPLLIC QKGILHKDSN MPMDMREFVL LFMTFDEKKS WYYEKKSRSS WRLTSSEMKK SHEFHAINGM IY SLPGLKM YEQEWVRLHL LNIGGSQDIH VVHFHGQTLL ENGNKQHQLG VWPLLPGSFK TLEMKASKPG WWLLNTEVGE NQR AGMQTP FLIMDRDCRM PMGLSTGIIS DSQIKASEFL GYWEPRLARL NNGGSYNAWS VEKLAAEFAS KPWIQVDMQK EVII TGIQT QGAKHYLKSC YTTEFYVAYS SNQINWQIFK GNSTRNVMYF NGNSDASTIK ENQFDPPIVA RYIRISPTRA YNRPT LRLE LQGCEVNGCS TPLGMENGKI ENKQITASSF KKSWWGDYWE PFRARLNAQG RVNAWQAKAN NNKQWLEIDL LKIKKI TAI ITQGCKSLSS EMYVKSYTIH YSEQGVEWKP YRLKSSMVDK IFEGNTNTKG HVKNFFNPPI ISRFIRVIPK TWNQSIA LR LELFGCDIY

UniProtKB: Coagulation factor V

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Macromolecule #3: Meizothrombin

MacromoleculeName: Meizothrombin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: thrombin
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.503898 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString:
VPDRGQQYQG RLAVTTHGLP CLAWASAQAK ALSKHQDFNS AVQLVENFCR NPDGDEEGVW CYVAGKPGDF GYCDLNYCEE AVEEETGDG LDEDSDRAIE GRTATSEYQT FFNPRTFGSG EADCGLRPLF EKKSLEDKTE RELLESYID

UniProtKB: Prothrombin

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Macromolecule #4: Thrombin heavy chain

MacromoleculeName: Thrombin heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: thrombin
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.578055 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: IVEGSDAEIG MSPWQVMLFR KSPQELLCGA SLISDRWVLT AAHCLLYPPW DKNFTENDLL VRIGKHSRTR YERNIEKISM LEKIYIHPR YNWRENLDRD IALMKLKKPV AFSDYIHPVC LPDRETAASL LQAGYKGRVT GWGNLKETWT ANVGKGQPSV L QVVNLPIV ...String:
IVEGSDAEIG MSPWQVMLFR KSPQELLCGA SLISDRWVLT AAHCLLYPPW DKNFTENDLL VRIGKHSRTR YERNIEKISM LEKIYIHPR YNWRENLDRD IALMKLKKPV AFSDYIHPVC LPDRETAASL LQAGYKGRVT GWGNLKETWT ANVGKGQPSV L QVVNLPIV ERPVCKDSTR IRITDNMFCA GYKPDEGKRG DACEGDAGGP FVMKSPFNNR WYQMGIVSWG EGCDRDGKYG FY THVFRLK KWIQKVIDQF

UniProtKB: Prothrombin

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Macromolecule #5: Coagulation factor V heavy chain

MacromoleculeName: Coagulation factor V heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.205906 KDa
SequenceString: 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 ST

UniProtKB: Coagulation factor V

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: Microscope is outfitted with a Cs image corrector with two hexapole elements.
DetailsPreliminary grid screening was performed manually.
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 3 / Number real images: 5179 / Average electron dose: 51.0 e/Å2 / Details: 28% of images collected at 30 degree stage tilt.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 150.0 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 38200
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial modelPDB ID:

3e6p


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9yq8:
Cryo-EM complex of meizothrombinDESF1, factor Xa, and factor Va

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Atomic model buiding 2

Initial modelPDB ID:

1xkb


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9yq8:
Cryo-EM complex of meizothrombinDESF1, factor Xa, and factor Va

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Atomic model buiding 3

Initial modelPDB ID:

8tn9


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9yq8:
Cryo-EM complex of meizothrombinDESF1, factor Xa, and factor Va

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