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- EMDB-77609: Coagulation factor V DTQQ, membrane-bound, on Ptd-choline : Ptd-s... -

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Basic information

Entry
Database: EMDB / ID: EMD-77609
TitleCoagulation factor V DTQQ, membrane-bound, on Ptd-choline : Ptd-serine 75:25 vesicles
Map data213K_J696_sharp_aligned.mrc Sharpened map B-factor applied -107 A2
Sample
  • Complex: Coagulation factor V DTQQ, glycosylated, bound to calcium (II), copper (I), and to phosphatidyl-L-serine headgroups in small unilamellar vesicles
    • Protein or peptide: Coagulation factor V
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: COPPER (I) ION
  • Ligand: PHOSPHOSERINE
  • Ligand: water
Keywordscoagulation factor V / phosphatidylserine / peripheral membrane protein / liposome / MEMBRANE PROTEIN
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 / : / 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 / : / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / Post-translational protein phosphorylation / blood coagulation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / extracellular vesicle / endoplasmic reticulum lumen / copper ion binding / : / 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. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain ...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. / 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: 2.9 Å
AuthorsKolyadko VN / Pumroy RA / Moiseenkova-Bell VY / Krishnaswamy S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01HL139420 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural basis for membrane binding by coagulation factors V and VIII and their specificity for phosphatidylserine-containing membranes.
Authors: Vladimir N Kolyadko / Ruth A Pumroy / Vera Y Moiseenkova-Bell / Sriram Krishnaswamy /
Abstract: Phosphatidylserine on the surface of activated cells serves as a signal for coagulation factor binding and the membrane-dependent assembly of enzyme complexes that drive the accelerated host response ...Phosphatidylserine on the surface of activated cells serves as a signal for coagulation factor binding and the membrane-dependent assembly of enzyme complexes that drive the accelerated host response to vascular damage. Here, we use single-particle cryo-EM of liposome-bound proteins to establish common mechanisms utilized by coagulation factors V and VIII for membrane binding and phospholipid specificity. The interface between these peripheral proteins and the membrane shows contacts between the discoidin C1 and C2 domains and the interfacial phospholipid headgroup region of the membrane bilayer. There is no evidence for the insertion of membrane-contacting protein loops into the membrane core. This refutes previous models of high affinity protein binding by insertion into the hydrophobic core of the membrane. We also resolve density for the headgroup of phosphatidylserine bound to conserved pockets within the C1 and C2 domains. These single binding pockets in each C domain highlight the network of putative hydrogen bonds that contribute to binding specificity for phosphatidylserine. Our results now provide a high-resolution structural view of the protein-membrane interface for these coagulation proteins and highlight the utility of using liposomes as near-physiologic membrane mimetics in structural studies. The principles established in this work may also apply to other biological systems wherein function is regulated by reversible membrane binding.
History
DepositionJun 13, 2026-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77609.png

Downloads & links

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Map

FileDownload / File: emd_77609.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation213K_J696_sharp_aligned.mrc Sharpened map B-factor applied -107 A2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.48
Minimum - Maximum-2.9838119 - 4.2292643
Average (Standard dev.)0.002972113 (±0.10081324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: J696 003 volume map.mrc Unsharpened map Membrane is seen at 0.14...

Fileemd_77609_additional_1.map
AnnotationJ696_003_volume_map.mrc Unsharpened map Membrane is seen at 0.14 contour
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 213K J696 half A.mrc half-1

Fileemd_77609_half_map_1.map
Annotation213K_J696_half_A.mrc half-1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 213K J696 half B.mrc half-2

Fileemd_77609_half_map_2.map
Annotation213K_J696_half_B.mrc half-2
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Coagulation factor V DTQQ, glycosylated, bound to calcium (II), c...

EntireName: Coagulation factor V DTQQ, glycosylated, bound to calcium (II), copper (I), and to phosphatidyl-L-serine headgroups in small unilamellar vesicles
Components
  • Complex: Coagulation factor V DTQQ, glycosylated, bound to calcium (II), copper (I), and to phosphatidyl-L-serine headgroups in small unilamellar vesicles
    • Protein or peptide: Coagulation factor V
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: COPPER (I) ION
  • Ligand: PHOSPHOSERINE
  • Ligand: water

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Supramolecule #1: Coagulation factor V DTQQ, glycosylated, bound to calcium (II), c...

SupramoleculeName: Coagulation factor V DTQQ, glycosylated, bound to calcium (II), copper (I), and to phosphatidyl-L-serine headgroups in small unilamellar vesicles
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Small unilamellar vesicles are composed of a mixture of phospholipids (phosphatidylcholine : phosphatidylserine 75:25)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 216 KDa

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Macromolecule #1: Coagulation factor V

MacromoleculeName: Coagulation factor V / type: protein_or_peptide / ID: 1 / Details: Single-chain; B-domain region 811-1491 deleted / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 173.755 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
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 AAALGIQSFR NSSLNQEE E EFNLTALALE NGTEFVSSNT DIIVGSNYSS PSNISKFTVN NLAEPQKAPS HQQATTAGSP LRHLIGKNSV LNSSTAEHS SPYSEDPIED TDYIEIIPKE EVQSSEDDYA EIDYVPYDDP YKTDVRTNIN SSRDPDNIAA WYLQSNNGNR RNYYIAAEEI SWDYSEFVQ RETDIEDSDD IPEDTTYKKV VFRKYLDSTF TKRDPRGEYE EHLGILGPII RAEVDDVIQV RFKNLASRPY S LHAHGLSY EKSSEGKTYE DDSPEWFKED NAVQPNSSYT YVWHATERSG PESPGSACRA WAYYSAVNPE KDIHSGLIGP LL ICQKGIL HKDSNMPVDM REFVLLFMTF DEKKSWYYEK KSRSSWRLTS SEMKKSHEFH AINGMIYSLP GLKMYEQEWV RLH LLNIGG SQDIHVVHFH GQTLLENGNK QHQLGVWPLL PGSFKTLEMK ASKPGWWLLN TEVGENQRAG MQTPFLIMDR DCRM PMGLS TGIISDSQIK ASEFLGYWEP RLARLNNGGS YNAWSVEKLA AEFASKPWIQ VDMQKEVIIT GIQTQGAKHY LKSCY TTEF YVAYSSNQIN WQIFKGNSTR NVMYFNGNSD ASTIKENQFD PPIVARYIRI SPTRAYNRPT LRLELQGCEV NGCSTP LGM ENGKIENKQI TASSFKKSWW GDYWEPFRAR LNAQGRVNAW QAKANNNKQW LEIDLLKIKK ITAIITQGCK SLSSEMY VK SYTIHYSEQG VEWKPYRLKS SMVDKIFEGN TNTKGHVKNF FNPPIISRFI RVIPKTWNQS ITLRLELFGC DIY

UniProtKB: Coagulation factor V

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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: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #6: COPPER (I) ION

MacromoleculeName: COPPER (I) ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: CU1
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU1:
COPPER (I) ION

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Macromolecule #7: PHOSPHOSERINE

MacromoleculeName: PHOSPHOSERINE / type: ligand / ID: 7 / Number of copies: 2 / Formula: SEP
Molecular weightTheoretical: 185.072 Da
Chemical component information

ChemComp-SEP:
PHOSPHOSERINE

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 5 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.1 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMsodium chlorideNaCl
2.0 mMcalcium chlorideCaCl2
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: double application and blotting.
DetailsProtein is mixed with prepared small unilamellar vesicles

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3766 / Average electron dose: 50.0 e/Å2 / Details: 41 frames per movie
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.1) / Number images used: 213000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-36jb:
Coagulation factor V DTQQ, membrane-bound, on Ptd-choline : Ptd-serine 75:25 vesicles

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