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- EMDB-26060: Cryo-em structure of human prothrombin:prothrombinase at 4.1 Angs... -

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Entry
Database: EMDB / ID: EMD-26060
TitleCryo-em structure of human prothrombin:prothrombinase at 4.1 Angstrom resolution
Map dataprothrombin:prothrombinase
Sample
  • Complex: prothrombin prothrombinase
    • Complex: Prothrombin (E.C.3.4.21.5), Factor X light chain, Activated factor Xa heavy chain
      • Protein or peptide: Prothrombin
      • Protein or peptide: Factor X light chain
      • Protein or peptide: Activated factor Xa heavy chain
    • Complex: Coagulation factor Va
      • Protein or peptide: Coagulation factor Va
      • Protein or peptide: Coagulation factor Va
Keywordsprothrombin prothrombinase / 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 / Extrinsic Pathway of Fibrin Clot Formation / COPII-mediated vesicle transport / blood circulation ...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 / Extrinsic Pathway of Fibrin Clot Formation / COPII-mediated vesicle transport / blood circulation / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin-activated receptor signaling pathway / thrombin / COPII-coated ER to Golgi transport vesicle / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / Defective F8 cleavage by thrombin / ligand-gated ion channel signaling pathway / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / positive regulation of collagen biosynthetic process / negative regulation of platelet activation / negative regulation of blood coagulation / positive regulation of blood coagulation / positive regulation of TOR signaling / negative regulation of fibrinolysis / regulation of cytosolic calcium ion concentration / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / negative regulation of cytokine production involved in inflammatory response / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of release of sequestered calcium ion into cytosol / Peptide ligand-binding receptors / platelet alpha granule lumen / Regulation of Complement cascade / acute-phase response / negative regulation of proteolysis / positive regulation of receptor signaling pathway via JAK-STAT / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / lipopolysaccharide binding / growth factor activity / positive regulation of insulin secretion / phospholipid binding / platelet activation / positive regulation of protein localization to nucleus / response to wounding / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / extracellular vesicle / heparin binding / regulation of cell shape / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of cell growth / : / G alpha (q) signalling events / blood microparticle / positive regulation of protein phosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of cell migration / receptor ligand activity / copper ion binding / endoplasmic reticulum lumen / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / positive regulation of cell population proliferation / calcium ion binding / proteolysis / extracellular space / extracellular exosome / 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. / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : ...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. / 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 / Coagulation Factor Xa inhibitory site / Multicopper oxidase, N-terminal / Multicopper oxidase / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) 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. / EGF-like domain signature 2. / Cupredoxin / 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: 4.1 Å
AuthorsDi Cera E / Ruben EA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: Blood / Year: 2022
Title: Cryo-EM structure of the prothrombin-prothrombinase complex.
Authors: Eliza A Ruben / Brock Summers / Michael J Rau / James A J Fitzpatrick / Enrico Di Cera /
Abstract: The intrinsic and extrinsic pathways of the coagulation cascade converge to a common step where the prothrombinase complex, comprising the enzyme factor Xa (fXa), the cofactor fVa, Ca2+ and ...The intrinsic and extrinsic pathways of the coagulation cascade converge to a common step where the prothrombinase complex, comprising the enzyme factor Xa (fXa), the cofactor fVa, Ca2+ and phospholipids, activates the zymogen prothrombin to the protease thrombin. The reaction entails cleavage at 2 sites, R271 and R320, generating the intermediates prethrombin 2 and meizothrombin, respectively. The molecular basis of these interactions that are central to hemostasis remains elusive. We solved 2 cryogenic electron microscopy (cryo-EM) structures of the fVa-fXa complex, 1 free on nanodiscs at 5.3-Å resolution and the other bound to prothrombin at near atomic 4.1-Å resolution. In the prothrombin-fVa-fXa complex, the Gla domains of fXa and prothrombin align on a plane with the C1 and C2 domains of fVa for interaction with membranes. Prothrombin and fXa emerge from this plane in curved conformations that bring their protease domains in contact with each other against the A2 domain of fVa. The 672ESTVMATRKMHDRLEPEDEE691 segment of the A2 domain closes on the protease domain of fXa like a lid to fix orientation of the active site. The 696YDYQNRL702 segment binds to prothrombin and establishes the pathway of activation by sequestering R271 against D697 and directing R320 toward the active site of fXa. The cryo-EM structure provides a molecular view of prothrombin activation along the meizothrombin pathway and suggests a mechanism for cleavage at the alternative R271 site. The findings advance our basic knowledge of a key step of coagulation and bear broad relevance to other interactions in the blood.
History
DepositionJan 25, 2022-
Header (metadata) releaseMay 4, 2022-
Map releaseMay 4, 2022-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26060.png

Downloads & links

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Map

FileDownload / File: emd_26060.map.gz / Format: CCP4 / Size: 874.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprothrombin:prothrombinase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.41 Å/pix.
x 612 pix.
= 252.756 Å		0.41 Å/pix.
x 612 pix.
= 252.756 Å		0.41 Å/pix.
x 612 pix.
= 252.756 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.413 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.13259314 - 0.22159648
Average (Standard dev.)0.00015992128 (±0.008420089)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions612612612
Spacing612612612
CellA=B=C: 252.756 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26060_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: prothrombin:prothrombinase

Fileemd_26060_half_map_1.map
Annotationprothrombin:prothrombinase
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: prothrombin:prothrombinase

Fileemd_26060_half_map_2.map
Annotationprothrombin:prothrombinase
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : prothrombin prothrombinase

EntireName: prothrombin prothrombinase
Components
  • Complex: prothrombin prothrombinase
    • Complex: Prothrombin (E.C.3.4.21.5), Factor X light chain, Activated factor Xa heavy chain
      • Protein or peptide: Prothrombin
      • Protein or peptide: Factor X light chain
      • Protein or peptide: Activated factor Xa heavy chain
    • Complex: Coagulation factor Va
      • Protein or peptide: Coagulation factor Va
      • Protein or peptide: Coagulation factor Va

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Supramolecule #1: prothrombin prothrombinase

SupramoleculeName: prothrombin prothrombinase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Prothrombin (E.C.3.4.21.5), Factor X light chain, Activated facto...

SupramoleculeName: Prothrombin (E.C.3.4.21.5), Factor X light chain, Activated factor Xa heavy chain
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2, #5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Coagulation factor Va

SupramoleculeName: Coagulation factor Va / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Prothrombin

MacromoleculeName: Prothrombin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: thrombin
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.370113 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
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 #2: Factor X light chain

MacromoleculeName: Factor X light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.743385 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString:
ANSFLEEMKK GHLERECMEE TCSYEEAREV FEDSDKTNEF WNKYKDGDQC ETSPCQNQGK CKDGLGEYTC TCLEGFEGKN CELFTRKLC SLDNGDCDQF CHEEQNSVVC SCARGYTLAD NGKACIPTGP YPCGKQTLER

UniProtKB: Coagulation factor X

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Macromolecule #3: Coagulation factor Va

MacromoleculeName: Coagulation factor Va / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 81.274391 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 STVMATRKMH DRLEPEDEES DADYDYQNRL AAALGIR

UniProtKB: Coagulation factor V

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Macromolecule #4: Coagulation factor Va

MacromoleculeName: Coagulation factor Va / type: protein_or_peptide / ID: 4 / 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 #5: Activated factor Xa heavy chain

MacromoleculeName: Activated factor Xa heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.534596 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: IVGGQECKDG ECPWQALLIN EENEGFCGGT ILSEFYILTA AHCLYQAKRF KVRVGDRNTE QEEGGEAVHE VEVVIKHNRF TKETYDFDI AVLRLKTPIT FRMNVAPACL PERDWAESTL MTQKTGIVSG FGRTHEKGRQ STRLKMLEVP YVDRNSCKLS S SFIITQNM ...String:
IVGGQECKDG ECPWQALLIN EENEGFCGGT ILSEFYILTA AHCLYQAKRF KVRVGDRNTE QEEGGEAVHE VEVVIKHNRF TKETYDFDI AVLRLKTPIT FRMNVAPACL PERDWAESTL MTQKTGIVSG FGRTHEKGRQ STRLKMLEVP YVDRNSCKLS S SFIITQNM FCAGYDTKQE DACQGDAGGP HVTRFKDTYF VTGIVSWGEG CARKGKYGIY TKVTAFLKWI DRSMKTRGLP KA KSHAPEV ITSSPLK

UniProtKB: Coagulation factor X

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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 / Details: 20mM Hepes, 150mM NaCl, 5mM CaCl2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7kve


Details: 7kve
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 330317
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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