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- EMDB-56052: Structure of human prothrombinase with prothrombin -

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Basic information

Entry
Database: EMDB / ID: EMD-56052
TitleStructure of human prothrombinase with prothrombin
Map data
Sample
  • Complex: Human prothrombinase in complex with prothrombin
    • Protein or peptide: Activated factor Xa heavy chain
    • Protein or peptide: Coagulation factor X
    • Protein or peptide: Coagulation factor V heavy chain
    • Protein or peptide: Coagulation factor V light chain
    • Protein or peptide: Prothrombin
  • Ligand: CALCIUM ION
  • Ligand: SODIUM ION
Keywordsprothrombinase / factor Va / factor Xa / prothrombin / 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 / blood circulation / negative regulation of astrocyte differentiation / : / thrombospondin receptor activity / thrombin / thrombin-activated receptor signaling pathway / Defective factor XII causes hereditary angioedema / 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) / positive regulation of collagen biosynthetic process / negative regulation of platelet activation / negative regulation of blood coagulation / negative regulation of fibrinolysis / positive regulation of blood coagulation / negative regulation of proteolysis / 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 / fibrinolysis / regulation of cytosolic calcium ion concentration / : / negative regulation of cytokine production involved in inflammatory response / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / Regulation of Complement cascade / positive regulation of release of sequestered calcium ion into cytosol / positive regulation of receptor signaling pathway via JAK-STAT / acute-phase response / Cell surface interactions at the vascular wall / Peptide ligand-binding receptors / growth factor activity / Post-translational protein phosphorylation / response to wounding / lipopolysaccharide binding / platelet activation / positive regulation of protein localization to nucleus / phospholipid binding / 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 / Platelet degranulation / heparin binding / extracellular vesicle / Thrombin signalling through proteinase activated receptors (PARs) / Dengue Virus-Host Interactions / antimicrobial humoral immune response mediated by antimicrobial peptide / blood microparticle / extracellular matrix / G alpha (q) signalling events / cell surface receptor signaling pathway / positive regulation of cell migration / endoplasmic reticulum lumen / receptor ligand activity / copper ion binding / serine-type endopeptidase activity / external side of plasma membrane / signaling receptor binding / calcium ion binding / 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 / : / Coagulation factor-like, Gla domain superfamily / F5/8 type C domain / 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 / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) 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. / Serine proteases, trypsin family, serine active site. / Peptidase S1A, chymotrypsin family / 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: 3.1 Å
AuthorsFaille A / Ustok FI / Warren A / Huntingon JA
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
British Heart FoundationRG/16/9/32391 United Kingdom
British Heart FoundationPG/24/11721 United Kingdom
Cancer Research UKDRCNPG-Jun24/100002 United Kingdom
CitationJournal: EMBO J / Year: 2026
Title: Prothrombinase processivity is conferred by substrate allostery.
Authors: Fatma Işık Üstok / Alexandre Faille / Alan J Warren / James A Huntington /
Abstract: The prothrombinase complex, comprised of factor (f) Xa and fVa, converts prothrombin to thrombin through sequential cleavage at two sites in a rapid and processive manner. The molecular basis of ...The prothrombinase complex, comprised of factor (f) Xa and fVa, converts prothrombin to thrombin through sequential cleavage at two sites in a rapid and processive manner. The molecular basis of prothrombin processing is an enzymatical mystery that to solve requires structural insight into how the substrate and intermediate bind to prothrombinase. Here we present two 3.1 Å cryo-EM structures of prothrombinase bound to prothrombin and to meizothrombin. The prothrombin complex revealed a surprising interaction between the end of the heavy chain of fVa with exosite I of prothrombin, accounting for 70% of the contact interface. Triggering of the zymogen-to-protease conformational change following cleavage at Arg320 alters all domain-domain and fVa interactions observed for prothrombin, and results in a large-scale rearrangement of meizothrombin that presents the second cleavage site (Arg271) for processing. Together, these structures reveal a remarkable enzymatic mechanism that requires the active participation of the substrate itself, and introduces a new paradigm of 'substrate allostery'.
History
DepositionDec 10, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56052.png

Downloads & links

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Map

FileDownload / File: emd_56052.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 384 pix.
= 318.413 Å		0.83 Å/pix.
x 384 pix.
= 318.413 Å		0.83 Å/pix.
x 384 pix.
= 318.413 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8292 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-21.229444999999998 - 45.626842000000003
Average (Standard dev.)-0.000000000004852 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.4128 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56052_msk_1.map
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AxesZYX

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Additional map: Composite map made of main map and prothrombin focused-refinement map

Fileemd_56052_additional_1.map
AnnotationComposite map made of main map and prothrombin focused-refinement map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Prothrombin focused-refinement map

Fileemd_56052_additional_2.map
AnnotationProthrombin focused-refinement map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_56052_half_map_1.map
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Half map: #1

Fileemd_56052_half_map_2.map
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Sample components

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Entire : Human prothrombinase in complex with prothrombin

EntireName: Human prothrombinase in complex with prothrombin
Components
  • Complex: Human prothrombinase in complex with prothrombin
    • Protein or peptide: Activated factor Xa heavy chain
    • Protein or peptide: Coagulation factor X
    • Protein or peptide: Coagulation factor V heavy chain
    • Protein or peptide: Coagulation factor V light chain
    • Protein or peptide: Prothrombin
  • Ligand: CALCIUM ION
  • Ligand: SODIUM ION

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Supramolecule #1: Human prothrombinase in complex with prothrombin

SupramoleculeName: Human prothrombinase in complex with prothrombin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Activated factor Xa heavy chain

MacromoleculeName: Activated factor Xa heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.773916 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IVGGQECKDG ECPWQALLIN EENEGFCGGT ILSEFYILTA AHCLYQAKRF KVRVGDRNTE QEEGGEAVHE VEVVIKHNRF TKETYDFDI AVLRLKTPIT FRMNVAPACL PERDWANETL MKQDTGIVSG FGRTHEKGRQ STRLKMLEVP YVDRHSCMLS S DFRITQNM ...String:
IVGGQECKDG ECPWQALLIN EENEGFCGGT ILSEFYILTA AHCLYQAKRF KVRVGDRNTE QEEGGEAVHE VEVVIKHNRF TKETYDFDI AVLRLKTPIT FRMNVAPACL PERDWANETL MKQDTGIVSG FGRTHEKGRQ STRLKMLEVP YVDRHSCMLS S DFRITQNM FCAGYDTKQE DACQGDAGGP HVTRFKDTYF VTGIVSWGEG CARKGKYGIY TKVTRFLKWI KRSMKTRGLP KA KSHAPEV ITSSPLK

UniProtKB: Coagulation factor X

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Macromolecule #2: Coagulation factor X

MacromoleculeName: Coagulation factor X / type: protein_or_peptide / ID: 2
Details: M17 construct with 17 mutations enhancing affinity towards factor V, first 85 residues truncated, catalytic mutation S195A
Number of copies: 1 / Enantiomer: LEVO / EC number: coagulation factor Xa
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.182554 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MRKLCRAFNG DCDQFCKRVQ SSVVCSCARG YTLADNGKAC IPTGPYPCGK QTLERRKRSV AQATSSSGEA PDSITWKPYD AADLDPTEN PFDLLDFNQT QPERGDNNLT R

UniProtKB: Coagulation factor X

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Macromolecule #3: Coagulation factor V heavy chain

MacromoleculeName: Coagulation factor V heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 81.514578 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 DS(TYS)EIFEPPE STVMATRKMH DRLEPEDEES DAD(TYS)D(TYS)QNRL AAALGI R

UniProtKB: Coagulation factor V

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Macromolecule #4: Coagulation factor V light chain

MacromoleculeName: Coagulation factor V light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.283008 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 #5: Prothrombin

MacromoleculeName: Prothrombin / type: protein_or_peptide / ID: 5 / Details: S195A mutation / Number of copies: 1 / Enantiomer: LEVO / EC number: thrombin
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.370113 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ANTFLEEVRK GNLERECVEE TCSYEEAFEA LESSTATDVF WAKYTACETA RTPRDKLAAC LEGNCAEGLG TNYRGHVNIT RSGIECQLW RSRYPHKPEI NSTTHPGADL QENFCRNPDS STTGPWCYTT DPTVRRQECS IPVCGQDQVT VAMTPRSEGS S VNLSPPLE ...String:
ANTFLEEVRK GNLERECVEE TCSYEEAFEA LESSTATDVF WAKYTACETA RTPRDKLAAC LEGNCAEGLG TNYRGHVNIT RSGIECQLW RSRYPHKPEI NSTTHPGADL QENFCRNPDS STTGPWCYTT DPTVRRQECS IPVCGQDQVT VAMTPRSEGS S VNLSPPLE QCVPDRGQQY QGRLAVTTHG LPCLAWASAQ AKALSKHQDF NSAVQLVENF CRNPDGDEEG VWCYVAGKPG DF GYCDLNY CEEAVEEETG DGLDEDSDRA IEGRTATSEY QTFFNPRTFG SGEADCGLRP LFEKKSLEDK TERELLESYI DGR IVEGSD AEIGMSPWQV MLFRKSPQEL LCGASLISDR WVLTAAHCLL YPPWDKNFTE NDLLVRIGKH SRTRYERNIE KISM LEKIY IHPRYNWREN LDRDIALMKL KKPVAFSDYI HPVCLPDRET AASLLQAGYK GRVTGWGNLK ETWTANVGKG QPSVL QVVN LPIVERPVCK DSTRIRITDN MFCAGYKPDE GKRGDACEGD AGGPFVMKSP FNNRWYQMGI VSWGEGCDRD GKYGFY THV FRLKKWIQKV IDQFGE

UniProtKB: Prothrombin

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Macromolecule #11: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #12: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 12 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9i2h

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 76039
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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