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- EMDB-77611: Coagulation factor VIII, full-length, membrane-bound, on Ptd-chol... -

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Basic information

Entry
Database: EMDB / ID: EMD-77611
TitleCoagulation factor VIII, full-length, membrane-bound, on Ptd-choline : Ptd-serine 75:25 vesicles
Map dataF8-vesicle_VK02-1_j049_postprocess.mrc Post-processed map. B-factor applied -56 A2
Sample
  • Complex: Coagulation factor VIII, glycosylated, bound to calcium (II) and copper (I), and to phosphatidyl-L-serine headgroups in small unilamellar vesicles
    • Protein or peptide: Coagulation factor VIII
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: COPPER (I) ION
  • Ligand: PHOSPHOSERINE
  • Ligand: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
  • Ligand: water
Keywordscoagulation factor VIII / discoidin / phosphatidylserine / liposome / MEMBRANE PROTEIN
Function / homology
Function and homology information


Defective F8 accelerates dissociation of the A2 domain / Defective F8 binding to the cell membrane / Defective F8 secretion / Defective F8 sulfation at Y1699 / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / Defective F8 binding to von Willebrand factor / blood coagulation, intrinsic pathway / Initiation of coagulation cascade / Amplification and propagation of coagulation cascade / Regulation of clotting cascade ...Defective F8 accelerates dissociation of the A2 domain / Defective F8 binding to the cell membrane / Defective F8 secretion / Defective F8 sulfation at Y1699 / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / Defective F8 binding to von Willebrand factor / blood coagulation, intrinsic pathway / Initiation of coagulation cascade / Amplification and propagation of coagulation cascade / Regulation of clotting cascade / Cargo concentration in the ER / COPII-coated ER to Golgi transport vesicle / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / COPII-mediated vesicle transport / Defective F8 cleavage by thrombin / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / Golgi lumen / blood coagulation / Platelet degranulation / oxidoreductase activity / endoplasmic reticulum lumen / copper ion binding / extracellular region / 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 / Multicopper oxidase, C-terminal / Multicopper oxidase / Coagulation factors 5/8 type C domain (FA58C) profile. ...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 / Multicopper oxidase, C-terminal / Multicopper oxidase / 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 VIII
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 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 14, 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_77611.png

Downloads & links

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Map

FileDownload / File: emd_77611.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationF8-vesicle_VK02-1_j049_postprocess.mrc Post-processed map. B-factor applied -56 A2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 288 pix.
= 255.456 Å		0.89 Å/pix.
x 288 pix.
= 255.456 Å		0.89 Å/pix.
x 288 pix.
= 255.456 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.887 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.055109438 - 0.082561724
Average (Standard dev.)-0.0000005718678 (±0.002358054)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 255.45601 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: j048 run class001.mrc Unsharpened map

Fileemd_77611_additional_1.map
Annotationj048_run_class001.mrc Unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: j048 run half2 class001 unfil.mrc half-2

Fileemd_77611_half_map_1.map
Annotationj048_run_half2_class001_unfil.mrc half-2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: j048 run half1 class001 unfil.mrc half-1

Fileemd_77611_half_map_2.map
Annotationj048_run_half1_class001_unfil.mrc half-1
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 VIII, glycosylated, bound to calcium (II) and ...

EntireName: Coagulation factor VIII, glycosylated, bound to calcium (II) and copper (I), and to phosphatidyl-L-serine headgroups in small unilamellar vesicles
Components
  • Complex: Coagulation factor VIII, glycosylated, bound to calcium (II) and copper (I), and to phosphatidyl-L-serine headgroups in small unilamellar vesicles
    • Protein or peptide: Coagulation factor VIII
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: COPPER (I) ION
  • Ligand: PHOSPHOSERINE
  • Ligand: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
  • Ligand: water

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Supramolecule #1: Coagulation factor VIII, glycosylated, bound to calcium (II) and ...

SupramoleculeName: Coagulation factor VIII, glycosylated, bound to calcium (II) and 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: 330 KDa

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Macromolecule #1: Coagulation factor VIII

MacromoleculeName: Coagulation factor VIII / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 265.061062 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: ATRRYYLGAV ELSWDYMQSD LGELPVDARF PPRVPKSFPF NTSVVYKKTL FVEFTDHLFN IAKPRPPWMG LLGPTIQAEV YDTVVITLK NMASHPVSLH AVGVSYWKAS EGAEYDDQTS QREKEDDKVF PGGSHTYVWQ VLKENGPMAS DPLCLTYSYL S HVDLVKDL ...String:
ATRRYYLGAV ELSWDYMQSD LGELPVDARF PPRVPKSFPF NTSVVYKKTL FVEFTDHLFN IAKPRPPWMG LLGPTIQAEV YDTVVITLK NMASHPVSLH AVGVSYWKAS EGAEYDDQTS QREKEDDKVF PGGSHTYVWQ VLKENGPMAS DPLCLTYSYL S HVDLVKDL NSGLIGALLV CREGSLAKEK TQTLHKFILL FAVFDEGKSW HSETKNSLMQ DRDAASARAW PKMHTVNGYV NR SLPGLIG CHRKSVYWHV IGMGTTPEVH SIFLEGHTFL VRNHRQASLE ISPITFLTAQ TLLMDLGQFL LFCHISSHQH DGM EAYVKV DSCPEEPQLR MKNNEEAEDY DDDLTDSEMD VVRFDDDNSP SFIQIRSVAK KHPKTWVHYI AAEEEDWDYA PLVL APDDR SYKSQYLNNG PQRIGRKYKK VRFMAYTDET FKTREAIQHE SGILGPLLYG EVGDTLLIIF KNQASRPYNI YPHGI TDVR PLYSRRLPKG VKHLKDFPIL PGEIFKYKWT VTVEDGPTKS DPRCLTRYYS SFVNMERDLA SGLIGPLLIC YKESVD QRG NQIMSDKRNV ILFSVFDENR SWYLTENIQR FLPNPAGVQL EDPEFQASNI MHSINGYVFD SLQLSVCLHE VAYWYIL SI GAQTDFLSVF FSGYTFKHKM VYEDTLTLFP FSGETVFMSM ENPGLWILGC HNSDFRNRGM TALLKVSSCD KNTGDYYE D SYEDISAYLL SKNNAIEPRS FSQNSRHPST RQKQFNATTI PENDIEKTDP WFAHRTPMPK IQNVSSSDLL MLLRQSPTP HGLSLSDLQE AKYETFSDDP SPGAIDSNNS LSEMTHFRPQ LHHSGDMVFT PESGLQLRLN EKLGTTAATE LKKLDFKVSS TSNNLISTI PSDNLAAGTD NTSSLGPPSM PVHYDSQLDT TLFGKKSSPL TESGGPLSLS EENNDSKLLE SGLMNSQESS W GKNVSSTE SGRLFKGKRA HGPALLTKDN ALFKVSISLL KTNKTSNNSA TNRKTHIDGP SLLIENSPSV WQNILESDTE FK KVTPLIH DRMLMDKNAT ALRLNHMSNK TTSSKNMEMV QQKKEGPIPP DAQNPDMSFF KMLFLPESAR WIQRTHGKNS LNS GQGPSP KQLVSLGPEK SVEGQNFLSE KNKVVVGKGE FTKDVGLKEM VFPSSRNLFL TNLDNLHENN THNQEKKIQE EIEK KETLI QENVVLPQIH TVTGTKNFMK NLFLLSTRQN VEGSYDGAYA PVLQDFRSLN DSTNRTKKHT AHFSKKGEEE NLEGL GNQT KQIVEKYACT TRISPNTSQQ NFVTQRSKRA LKQFRLPLEE TELEKRIIVD DTSTQWSKNM KHLTPSTLTQ IDYNEK EKG AITQSPLSDC LTRSHSIPQA NRSPLPIAKV SSFPSIRPIY LTRVLFQDNS SHLPAASYRK KDSGVQESSH FLQGAKK NN LSLAILTLEM TGDQREVGSL GTSATNSVTY KKVENTVLPK PDLPKTSGKV ELLPKVHIYQ KDLFPTETSN GSPGHLDL V EGSLLQGTEG AIKWNEANRP GKVPFLRVAT ESSAKTPSKL LDPLAWDNHY GTQIPKEEWK SQEKSPEKTA FKKKDTILS LNACESNHAI AAINEGQNKP EIEVTWAKQG RTERLCSQNP PVLKRHQREI TRTTLQSDQE EIDYDDTISV EMKKEDFDIY DEDENQSPR SFQKKTRHYF IAAVERLWDY GMSSSPHVLR NRAQSGSVPQ FKKVVFQEFT DGSFTQPLYR GELNEHLGLL G PYIRAEVE DNIMVTFRNQ ASRPYSFYSS LISYEEDQRQ GAEPRKNFVK PNETKTYFWK VQHHMAPTKD EFDCKAWAYF SD VDLEKDV HSGLIGPLLV CHTNTLNPAH GRQVTVQEFA LFFTIFDETK SWYFTENMER NCRAPCNIQM EDPTFKENYR FHA INGYIM DTLPGLVMAQ DQRIRWYLLS MGSNENIHSI HFSGHVFTVR KKEEYKMALY NLYPGVFETV EMLPSKAGIW RVEC LIGEH LHAGMSTLFL VYSNKCQTPL GMASGHIRDF QITASGQYGQ WAPKLARLHY SGSINAWSTK EPFSWIKVDL LAPMI IHGI KTQGARQKFS SLYISQFIIM YSLDGKKWQT YRGNSTGTLM VFFGNVDSSG IKHNIFNPPI IARYIRLHPT HYSIRS TLR MELMGCDLNS CSMPLGMESK AISDAQITAS SYFTNMFATW SPSKARLHLQ GRSNAWRPQV NNPKEWLQVD FQKTMKV TG VTTQGVKSLL TSMYVKEFLI SSSQDGHQWT LFFQNGKVKV FQGNQDSFTP VVNSLDPPLL TRYLRIHPQS WVHQIALR M EVLGCEAQDL Y

UniProtKB: Coagulation factor VIII

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

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

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

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: COPPER (I) ION

MacromoleculeName: COPPER (I) ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CU1
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU1:
COPPER (I) ION

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Macromolecule #5: PHOSPHOSERINE

MacromoleculeName: PHOSPHOSERINE / type: ligand / ID: 5 / Number of copies: 2 / Formula: SEP
Molecular weightTheoretical: 185.072 Da
Chemical component information

ChemComp-SEP:
PHOSPHOSERINE

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Macromolecule #6: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE

MacromoleculeName: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
type: ligand / ID: 6 / Number of copies: 1 / Formula: CPS
Molecular weightTheoretical: 614.877 Da
Chemical component information

ChemComp-CPS:
3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / detergent*YM

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 1 / 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
5.0 mMcalcium chlorideCaCl2
0.2 mMCHAPS
GridModel: UltrAuFoil R0./1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
DetailsProtein is mixed with prepared small unilamellar vesicles

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 9197 / Average electron dose: 39.64 e/Å2
Electron beamAcceleration voltage: 200 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: 130000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 212413
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-36jl:
Coagulation factor VIII, full-length, membrane-bound, on Ptd-choline : Ptd-serine 75:25 vesicles

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