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- EMDB-23048: Cryo-EM structure of human Factor V at 3.3 Angstrom resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-23048
TitleCryo-EM structure of human Factor V at 3.3 Angstrom resolution
Map data
Sample
  • Complex: human Factor V
    • Protein or peptide: Coagulation factor V
Keywordshuman Factor V / BLOOD CLOTTING
Function / homology
Function and homology information


response to vitamin K / platelet alpha granule / Cargo concentration in the ER / COPII-coated ER to Golgi transport vesicle / COPII-mediated vesicle transport / blood circulation / 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 / COPII-coated ER to Golgi transport vesicle / COPII-mediated vesicle transport / blood circulation / 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 / Platelet degranulation / extracellular vesicle / endoplasmic reticulum lumen / copper ion binding / 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. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain ...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. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Coagulation factor V
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsRuben EA / Di Cera E
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: 2021
Title: Cryo-EM structures of human coagulation factors V and Va.
Authors: Eliza A Ruben / Michael J Rau / James A J Fitzpatrick / Enrico Di Cera /
Abstract: Coagulation factor V (fV) is the precursor of fVa, which, together with fXa, Ca2+, and phospholipids, defines the prothrombinase complex and activates prothrombin in the penultimate step of the ...Coagulation factor V (fV) is the precursor of fVa, which, together with fXa, Ca2+, and phospholipids, defines the prothrombinase complex and activates prothrombin in the penultimate step of the coagulation cascade. We solved the cryogenic electron microscopy (cryo-EM) structures of human fV and fVa at atomic (3.3 Å) and near-atomic (4.4 Å) resolution, respectively. The structure of fV reveals the entire A1-A2-B-A3-C1-C2 assembly, but with a surprisingly disordered B domain. The C1 and C2 domains provide a platform for interaction with phospholipid membranes and support the A1 and A3 domains, with the A2 domain sitting on top of them. The B domain is highly dynamic and visible only for short segments connecting to the A2 and A3 domains. The A2 domain reveals all sites of proteolytic processing by thrombin and activated protein C, a partially buried epitope for binding fXa, and fully exposed epitopes for binding activated protein C and prothrombin. Removal of the B domain and activation to fVa exposes the sites of cleavage by activated protein C at R306 and R506 and produces increased disorder in the A1-A2-A3-C1-C2 assembly, especially in the C-terminal acidic portion of the A2 domain that is responsible for prothrombin binding. Ordering of this region and full exposure of the fXa epitope emerge as necessary steps in the assembly of the prothrombin-prothrombinase complex. These structures offer molecular context for the function of fV and fVa and pioneer the analysis of coagulation factors by cryo-EM.
History
DepositionNov 27, 2020-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.43
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.43
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7kve
  • Surface level: 0.43
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23048.png

Downloads & links

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Map

FileDownload / File: emd_23048.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 296 pix.
= 325.6 Å		1.1 Å/pix.
x 296 pix.
= 325.6 Å		1.1 Å/pix.
x 296 pix.
= 325.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.43 / Movie #1: 0.43
Minimum - Maximum-1.628795 - 2.803443
Average (Standard dev.)0.00015107563 (±0.06669357)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 325.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z296296296
origin x/y/z0.0000.0000.000
length x/y/z325.600325.600325.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS296296296
D min/max/mean-1.6292.8030.000

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Supplemental data

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Mask #1

Fileemd_23048_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_23048_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_23048_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : human Factor V

EntireName: human Factor V
Components
  • Complex: human Factor V
    • Protein or peptide: Coagulation factor V

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Supramolecule #1: human Factor V

SupramoleculeName: human Factor V / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Coagulation factor V

MacromoleculeName: Coagulation factor V / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 248.973234 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 AAALGIRSFR NSSLNQEE E EFNLTALALE NGTEFVSSNT DIIVGSNYSS PSNISKFTVN NLAEPQKAPS HQQATTAGSP LRHLIGKNSV LNSSTAEHS SPYSEDPIED PLQPDVTGIR LLSLGAGEFK SQEHAKHKGP KVERDQAAKH RFSWMKLLAH KVGRHLSQDT GSPSGMRPWE DLPSQDTGS PSRMRPWKDP PSDLLLLKQS NSSKILVGRW HLASEKGSYE IIQDTDEDTA VNNWLISPQN ASRAWGESTP L ANKPGKQS GHPKFPRVRH KSLQVRQDGG KSRLKKSQFL IKTRKKKKEK HTHHAPLSPR TFHPLRSEAY NTFSERRLKH SL VLHKSNE TSLPTDLNQT LPSMDFGWIA SLPDHNQNSS NDTGQASCPP GLYQTVPPEE HYQTFPIQDP DQMHSTSDPS HRS SSPELS EMLEYDRSHK SFPTDISQMS PSSEHEVWQT VISPDLSQVT LSPELSQTNL SPDLSHTTLS PELIQRNLSP ALGQ MPISP DLSHTTLSPD LSHTTLSLDL SQTNLSPELS QTNLSPALGQ MPLSPDLSHT TLSLDFSQTN LSPELSHMTL SPELS QTNL SPALGQMPIS PDLSHTTLSL DFSQTNLSPE LSQTNLSPAL GQMPLSPDPS HTTLSLDLSQ TNLSPELSQT NLSPDL SEM PLFADLSQIP LTPDLDQMTL SPDLGETDLS PNFGQMSLSP DLSQVTLSPD ISDTTLLPDL SQISPPPDLD QIFYPSE SS QSLLLQEFNE SFPYPDLGQM PSPSSPTLND TFLSKEFNPL VIVGLSKDGT DYIEIIPKEE VQSSEDDYAE IDYVPYDD P YKTDVRTNIN SSRDPDNIAA WYLRSNNGNR RNYYIAAEEI SWDYSEFVQR ETDIEDSDDI PEDTTYKKVV FRKYLDSTF TKRDPRGEYE EHLGILGPII RAEVDDVIQV RFKNLASRPY SLHAHGLSYE KSSEGKTYED DSPEWFKEDN AVQPNSSYTY VWHATERSG PESPGSACRA WAYYSAVNPE KDIHSGLIGP LLICQKGILH KDSNMPMDMR EFVLLFMTFD EKKSWYYEKK S RSSWRLTS SEMKKSHEFH AINGMIYSLP GLKMYEQEWV RLHLLNIGGS QDIHVVHFHG QTLLENGNKQ HQLGVWPLLP GS FKTLEMK ASKPGWWLLN TEVGENQRAG MQTPFLIMDR DCRMPMGLST GIISDSQIKA SEFLGYWEPR LARLNNGGSY NAW SVEKLA AEFASKPWIQ VDMQKEVIIT GIQTQGAKHY LKSCYTTEFY VAYSSNQINW QIFKGNSTRN VMYFNGNSDA STIK ENQFD PPIVARYIRI SPTRAYNRPT LRLELQGCEV NGCSTPLGME NGKIENKQIT ASSFKKSWWG DYWEPFRARL NAQGR VNAW QAKANNNKQW LEIDLLKIKK ITAIITQGCK SLSSEMYVKS YTIHYSEQGV EWKPYRLKSS MVDKIFEGNT NTKGHV KNF FNPPIISRFI RVIPKTWNQS IALRLELFGC DIY

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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 1.65 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 299182
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-7kve:
Cryo-EM structure of human Factor V at 3.3 Angstrom resolution

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