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- EMDB-61327: Structure of Engineered Coagulation Factor VIII with Enhanced Sec... -

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Basic information

Entry
Database: EMDB / ID: EMD-61327
TitleStructure of Engineered Coagulation Factor VIII with Enhanced Secretion and Coagulation Potential
Map dataunsharpened map
Sample
  • Complex: Engineered Coagulation Factor VIII with Enhanced Secretion and Coagulation Potential
    • Protein or peptide: Coagulation factor VIII
Keywordshemophilia / BLOOD CLOTTING
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 / Cargo concentration in the ER / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant ...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 / Cargo concentration in the ER / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / COPII-coated ER to Golgi transport vesicle / COPII-mediated vesicle transport / Defective F8 cleavage by thrombin / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Golgi lumen / blood coagulation / Platelet degranulation / oxidoreductase activity / endoplasmic reticulum lumen / copper ion binding / extracellular space / extracellular region / 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. / Multicopper oxidase, C-terminal / Multicopper oxidase ...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. / Multicopper oxidase, C-terminal / Multicopper oxidase / 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: 3.17 Å
AuthorsKio H / Osamu N / Tsukasa O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: To Be Published
Title: Engineered Coagulation Factor VIII with Enhanced Secretion and Coagulation Potential for Hemophilia Gene Therapy
Authors: Yuji K / Yuto N / Kio H / Tiago L / Yuma F / Yuki Y / Nemekhbayar B / Morisada H / Yuko K / Susumu U / Osamu N / Keiji N / Tsukasa O
History
DepositionAug 27, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61327.png

Downloads & links

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Map

FileDownload / File: emd_61327.map.gz / Format: CCP4 / Size: 14.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 156 pix.
= 172.645 Å		1.11 Å/pix.
x 156 pix.
= 172.645 Å		1.11 Å/pix.
x 156 pix.
= 172.645 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.10909623 - 0.29203698
Average (Standard dev.)-0.001702833 (±0.011236227)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin343434
Dimensions156156156
Spacing156156156
CellA=B=C: 172.64519 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61327_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61327_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61327_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Engineered Coagulation Factor VIII with Enhanced Secretion and Co...

EntireName: Engineered Coagulation Factor VIII with Enhanced Secretion and Coagulation Potential
Components
  • Complex: Engineered Coagulation Factor VIII with Enhanced Secretion and Coagulation Potential
    • Protein or peptide: Coagulation factor VIII

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Supramolecule #1: Engineered Coagulation Factor VIII with Enhanced Secretion and Co...

SupramoleculeName: Engineered Coagulation Factor VIII with Enhanced Secretion and Coagulation Potential
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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: 167.452469 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQIELSTCFF LCLLPFCFSA TRRYYLGAVE LSWDYMQSDL GELHVDTRFP PRVPKSFPFN TSVVYKKTLF VEFTDHLFNI AKPRPPWMG LLGPTIQAEV YDTVVITLKN MASHPVSLHA VGVSYWKASE GAEYDDQTSQ REKEDDKVFP GGSHTYVWQV L KENGPMAS ...String:
MQIELSTCFF LCLLPFCFSA TRRYYLGAVE LSWDYMQSDL GELHVDTRFP PRVPKSFPFN TSVVYKKTLF VEFTDHLFNI AKPRPPWMG LLGPTIQAEV YDTVVITLKN MASHPVSLHA VGVSYWKASE GAEYDDQTSQ REKEDDKVFP GGSHTYVWQV L KENGPMAS DPPCLTYSYL SHVDLVKDLN SGLIGALLVC REGSLAKEKT QTLHKFILLF AVFDEGKSWH SETNNSLTQD RD AASARAQ PKMHTVNGYV NRSLPGLIGC HRKSVYWHVI GMGTTPEVHS IFLEGHTFLV RNHRQASLEI SPITFLTAQT LLM DLGQFL LFCHISSHQH DGMEAYVKVD SCPEEPQLRM KNNEEAEDYD DDLTDSEMDV VRFDDDNSPP FIQIRSVAKK HPKT WVHYI AAEEEDWDYA PLVLAPDDRS YKSLYLNNGP QRIGRKYKKV RFMAYTDETF KTREAIQHES GILGPLLYGE VGDTL LIIF KNQASRPYNI YPHGITDVRP LHSGRLPKGV KHLKDMPILP GEIFKYKWTV TVEDGPTKSD PRCLTRYYSS FVNLER DLA SGLIGPLLIC YKESVDQRGN QMMSDKRNVI LFSVFDENRS WYLTENIQRF LPNPAGVQPE DPEFQASNIM HSINGYV FD SLQLSVCLHE VAYWYILSVG AQTDFLSVFF SGYTFKHKMV YEDTLTLFPF SGETVFMSME NPGLWILGCH NSDFRNRG M TALLKVSSCD KNTGDYYEDS YEDIPAYLLS KNNVIEPRSF SQNPPVLKRH QREITRTTLQ PDEEKIDYDD TFSVEMKKE DFDIYGEDEN QSPRSFQKKT RHYFIAAVER LWDYGMSSSP HVLRNRAQSG SVPQFKKVVF QEFTDGSFTQ PLYRGELNEH LGLLGPYIR AEVEDNIMVT FKNQASRPYS FYSSLISYEE DQRQGAEPRK NFVKPNETKT YFWKVQHHMA PTKDEFDCKA W AYFSDVDL EKDVHSGLIG PLLVCRTNTL NPAHGRQVTV QEFALFFTIF DETKSWYFTE NMERNCRAPC NIQMEDPTFK EN YRFHAIN GYIMDTLPGL VMAQDQRIRW YLLSMGSNEN IHSIHFSGHV FTVRKKEEYK MALYNLYPGV FETVEMLPSK VGI WRVECL IGEHLQAGMS TLFLVYSKKC QTPLGMASGH IRDFQITASG QYGQWAPKLA RLHYSGSINA WSTKEPFSWI KVDL LAPMI IHGIMTQGAR QKFSSLYISQ FIIMYSLDGK KWQTYRGNST GTLMVFFGNV DSSGIKHNIF NPPIIARYIR LHPTH YSIR STLRMELMGC DLNSCSMPLG MESKAISDAQ ITASSYLTNM FATWSPSQAR LHLQGRSNAW RPQVNNPKEW LQVDFQ KTM KVTGVTTQGV KSLLTSMYVK EFLISSSQDG HQWTLFLQNG KVKVFQGNQD SFTPVVNALD PPLLTRYLRI HPQSWAH HI ALRLEVLGCE AQDLY

UniProtKB: Coagulation factor VIII, Coagulation factor VIII

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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: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
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: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 218890
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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