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- EMDB-48481: Cryo-EM structure of factor Va bound to activated protein C -

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Basic information

Entry
Database: EMDB / ID: EMD-48481
TitleCryo-EM structure of factor Va bound to activated protein C
Map dataDeepEmhancer map. This map was used for model building
Sample
  • Complex: Complex of coagulation Factor Va and Activated Protein C
    • Complex: Coagulation Factor Va
      • Protein or peptide: Coagulation factor Va heavy chain
      • Protein or peptide: Coagulation factor Va light chain
    • Complex: Activated Protein C
      • Protein or peptide: Vitamin K-dependent protein C heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsCoagulation / Activated Factor V / Activated Protein C / BLOOD CLOTTING
Function / homology
Function and homology information


activated protein C (thrombin-activated peptidase) / positive regulation of establishment of endothelial barrier / negative regulation of coagulation / response to vitamin K / platelet alpha granule / Cargo concentration in the ER / COPII-mediated vesicle transport / blood circulation / COPII-coated ER to Golgi transport vesicle / negative regulation of blood coagulation ...activated protein C (thrombin-activated peptidase) / positive regulation of establishment of endothelial barrier / negative regulation of coagulation / response to vitamin K / platelet alpha granule / Cargo concentration in the ER / COPII-mediated vesicle transport / blood circulation / COPII-coated ER to Golgi transport vesicle / negative regulation of blood coagulation / 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 / Intrinsic Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / Golgi lumen / negative regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / extracellular vesicle / copper ion binding / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / negative regulation of apoptotic process / endoplasmic reticulum / Golgi apparatus / proteolysis / extracellular space / 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 / Coagulation Factor Xa inhibitory site / Multicopper oxidase, N-terminal / Multicopper oxidase / 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 / 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. / 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
Vitamin K-dependent protein C / Coagulation factor V
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsMohammed 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, HL139554 and HL147821 United States
Childrens Discovery Institute of Washington University and St. Louis Childrens HospitalCDI-CORE-2015-505 and CDI-CORE-2019-813 United States
The Foundation for Barnes-Jewish Hospital3770 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK020579 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA091842 United States
CitationJournal: Blood / Year: 2025
Title: Cryo-EM structure of coagulation factor Va bound to activated protein C.
Authors: Bassem M Mohammed / Katherine Basore / Enrico Di Cera /
Abstract: Coagulation factor Va (fVa) is the cofactor component of the prothrombinase complex required for rapid generation of thrombin from prothrombin in the penultimate step of the coagulation cascade. In ...Coagulation factor Va (fVa) is the cofactor component of the prothrombinase complex required for rapid generation of thrombin from prothrombin in the penultimate step of the coagulation cascade. In addition, fVa is a target for proteolytic inactivation by activated protein C (APC). Like other protein-protein interactions in the coagulation cascade, the fVa-APC interaction has long posed a challenge to structural biology and its molecular underpinnings remain unknown. A recent cryogenic electron microscopy (cryo-EM) structure of fVa has revealed the arrangement of its A1-A2-A3-C1-C2 domains and the environment of the sites of APC cleavage at R306 and R506. Here we report the cryo-EM structure of the fVa-APC complex at 3.15 Å resolution where the protease domain of APC engages R506 in the A2 domain of fVa mainly through electrostatic interactions between positively charged residues in the 30- and 70- loops of APC and an electronegative surface of fVa. The auxiliary Gla and EGF domains of APC are highly dynamic and point to solvent, without making contacts with fVa. Binding of APC displaces a large portion of the A2 domain of fVa and projects the 654VKCIPDDDEDSYEIFEP670 segment as a "latch", or exosite ligand, over the 70-loop of the enzyme. The latch induces a large conformational change of the autolysis loop of APC which in turn promotes docking of R506 into the primary specificity pocket. The cryo-EM structure of the fVa-APC complex validates the bulk of existing biochemical data and offers molecular context for a key regulatory interaction of the coagulation cascade.
History
DepositionDec 27, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48481.png

Downloads & links

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Map

FileDownload / File: emd_48481.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEmhancer map. This map was used for model building
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 420 pix.
= 365.442 Å		0.87 Å/pix.
x 420 pix.
= 365.442 Å		0.87 Å/pix.
x 420 pix.
= 365.442 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8701 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.185
Minimum - Maximum-0.001922941 - 2.9750395
Average (Standard dev.)0.0015454137 (±0.031096907)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 365.44202 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48481_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D Flex map generated using custom mesh defining...

Fileemd_48481_additional_1.map
Annotation3D Flex map generated using custom mesh defining each domain of the complex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D Flex map generated using custom mesh defining...

Fileemd_48481_additional_2.map
Annotation3D Flex map generated using custom mesh defining each domain of the complex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 3D flex half-maps

Fileemd_48481_half_map_1.map
Annotation3D flex half-maps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 3D flex half-maps

Fileemd_48481_half_map_2.map
Annotation3D flex half-maps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of coagulation Factor Va and Activated Protein C

EntireName: Complex of coagulation Factor Va and Activated Protein C
Components
  • Complex: Complex of coagulation Factor Va and Activated Protein C
    • Complex: Coagulation Factor Va
      • Protein or peptide: Coagulation factor Va heavy chain
      • Protein or peptide: Coagulation factor Va light chain
    • Complex: Activated Protein C
      • Protein or peptide: Vitamin K-dependent protein C heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of coagulation Factor Va and Activated Protein C

SupramoleculeName: Complex of coagulation Factor Va and Activated Protein C
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Coagulation activated Factor V (FVa) [from plasma] complex with Activated Protein C (APC) [made recombinantly with Ser360Ala mutation].

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Supramolecule #2: Coagulation Factor Va

SupramoleculeName: Coagulation Factor Va / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human) / Tissue: Blood

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Supramolecule #3: Activated Protein C

SupramoleculeName: Activated Protein C / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Coagulation factor Va heavy chain

MacromoleculeName: Coagulation factor Va heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: blood
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 #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) / Tissue: Blood
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: Vitamin K-dependent protein C heavy chain

MacromoleculeName: Vitamin K-dependent protein C heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: Blood
Molecular weightTheoretical: 26.949836 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: LIDGKMTRRG DSPWQVVLLD SKKKLACGAV LIHPSWVLTA AHCMDESKKL LVRLGEYDLR RWEKWELDLD IKEVFVHPNY SKSTTDNDI ALLHLAQPAT LSQTIVPICL PDSGLAEREL NQAGQETLVT GWGYHSSREK EAKRNRTFVL NFIKIPVVPH N ECSEVMSN ...String:
LIDGKMTRRG DSPWQVVLLD SKKKLACGAV LIHPSWVLTA AHCMDESKKL LVRLGEYDLR RWEKWELDLD IKEVFVHPNY SKSTTDNDI ALLHLAQPAT LSQTIVPICL PDSGLAEREL NQAGQETLVT GWGYHSSREK EAKRNRTFVL NFIKIPVVPH N ECSEVMSN MVSENMLCAG ILGDRQDACE GDAGGPMVAS FHGTWFLVGL VSWGEGCGLL HNYGVYTKVS RYLDWIHGHI RD

UniProtKB: Vitamin K-dependent protein C

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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 #1

Preparation ID1
Concentration0.1 mg/mL
BufferpH: 7.4 / Details: 20 mM HEPES, 150 mM NaCl, 5 mM CaCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Film type ID: 1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR / Details: Grids were coated with polylysine
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details0.1 mg/mL

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Sample preparation #2

Preparation ID2
Concentration0.1 mg/mL
BufferpH: 7.4 / Details: 20 mM HEPES, 150 mM NaCl, 5 mM CaCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Film type ID: 1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR / Details: Grids were coated with polylysine
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Sample preparation #3

Preparation ID3
Concentration0.1 mg/mL
BufferpH: 7.4 / Details: 20 mM HEPES, 150 mM NaCl, 5 mM CaCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Film type ID: 1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR / Details: Grids were coated with polylysine
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON IV (4k x 4k) / #0 - Detector mode: COUNTING / #0 - Digitization - Dimensions - Width: 4096 pixel / #0 - Digitization - Dimensions - Height: 4096 pixel / #0 - Number grids imaged: 1 / #0 - Number real images: 3193 / #0 - Average electron dose: 51.86 e/Å2 / #0 - Details: 30 degrees tilt / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON IV (4k x 4k) / #1 - Digitization - Dimensions - Width: 4096 pixel / #1 - Digitization - Dimensions - Height: 4096 pixel / #1 - Number grids imaged: 1 / #1 - Number real images: 600 / #1 - Average electron dose: 46.6 e/Å2 / #2 - Image recording ID: 3 / #2 - Film or detector model: FEI FALCON IV (4k x 4k) / #2 - Digitization - Dimensions - Width: 4096 pixel / #2 - Digitization - Dimensions - Height: 4096 pixel / #2 - Number grids imaged: 1 / #2 - Number real images: 2655 / #2 - Average electron dose: 46.89 e/Å2 / #2 - Details: 30 degrees tilt / #3 - Image recording ID: 4 / #3 - Film or detector model: FEI FALCON IV (4k x 4k) / #3 - Digitization - Dimensions - Width: 4096 pixel / #3 - Digitization - Dimensions - Height: 4096 pixel / #3 - Number grids imaged: 1 / #3 - Number real images: 2379 / #3 - Average electron dose: 47.19 e/Å2 / #4 - Image recording ID: 5 / #4 - Film or detector model: FEI FALCON IV (4k x 4k) / #4 - Digitization - Dimensions - Width: 4096 pixel / #4 - Digitization - Dimensions - Height: 4096 pixel / #4 - Number grids imaged: 1 / #4 - Number real images: 420 / #4 - Average electron dose: 46.89 e/Å2 / #5 - Image recording ID: 6 / #5 - Film or detector model: FEI FALCON IV (4k x 4k) / #5 - Digitization - Dimensions - Width: 4096 pixel / #5 - Digitization - Dimensions - Height: 4096 pixel / #5 - Number grids imaged: 1 / #5 - Number real images: 3210 / #5 - Average electron dose: 52.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.5 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

Image recording ID1
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2)
Details: 3D flex with custom mesh was used for the reconstruction
Number images used: 384239
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8tn9

source_name: PDB, initial_model_type: experimental model

9cth

source_name: PDB, initial_model_type: experimental model

1aut

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9mot:
Cryo-EM structure of factor Va bound to activated protein C

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