[English] 日本語
Yorodumi
- EMDB-71095: Nanodisc-embedded human TF/FVIIa/XK1 in complex with 10H10 Fab (3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71095
TitleNanodisc-embedded human TF/FVIIa/XK1 in complex with 10H10 Fab (3D Flexible Refinement)
Map dataNanodisc-embedded human TF/FVIIa/XK1 in complex with 10H10 Fab (3DFlex)
Sample
  • Complex: Complex of factor VIIa, XK1 and the Fab fragment of antibody 10H10, all bound to tissue factor embedded in a nanodisc membrane bilayer.
    • Complex: Human 10H10 antibody Fab
      • Protein or peptide: Human 10H10 antibody Fab heavy chain
      • Protein or peptide: Human 10H10 antibody Fab light chain
    • Complex: XK1 chimeric protein
      • Protein or peptide: Human factor X (FX) light chain
      • Protein or peptide: Human TFPI Kunitz domain 1 (K1)
    • Complex: Human activated FVIIa
      • Protein or peptide: Human factor VIIa - light chain
      • Protein or peptide: Human factor VIIa (FVIIa) protease domain
    • Complex: Human MBP-tagged tissue factor
      • Protein or peptide: Human tissue factor (TF)
Keywordscomplex / nanodisc / blood clotting
Biological speciesMus musculus (house mouse) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsPhotenhauer AL / Sedzro JC / Morrissey JH / Ohi MD
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R35 HL135823 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R35 HL171334 United States
National Institutes of Health/Office of the DirectorS10OD030275 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R24 GM145965 United States
American Heart AssociationN028347 United States
CitationJournal: Blood / Year: 2025
Title: Cryo-EM structure of the tissue factor/factor VIIa complex with a factor X mimetic reveals a novel allosteric mechanism.
Authors: Josepha C Sedzro / Amanda L Photenhauer / Fabienne Birkle / Katarina Meze / Alex Mortenson / Cade Duckworth / Po-Chao Wen / Sarah Kearns / Michael A Cianfrocco / Emad Tajkhorshid / Melanie D ...Authors: Josepha C Sedzro / Amanda L Photenhauer / Fabienne Birkle / Katarina Meze / Alex Mortenson / Cade Duckworth / Po-Chao Wen / Sarah Kearns / Michael A Cianfrocco / Emad Tajkhorshid / Melanie D Ohi / James H Morrissey /
Abstract: Blood clotting is triggered in hemostasis and thrombosis when the membrane-bound tissue factor (TF)/factor VIIa (FVIIa) complex activates factor X (FX). There are no structures of TF/FVIIa on ...Blood clotting is triggered in hemostasis and thrombosis when the membrane-bound tissue factor (TF)/factor VIIa (FVIIa) complex activates factor X (FX). There are no structures of TF/FVIIa on membranes, with or without FX. Using cryo-EM to address this gap, we assembled TF/FVIIa complexes on nanoscale membrane bilayers (nanodiscs), bound to XK1 and an antibody fragment. XK1 is a FX mimetic whose protease domain is replaced by the first Kunitz-type (K1) domain of tissue factor pathway inhibitor, while 10H10 is a non-inhibitory, anti-TF antibody. We determined a cryo-EM structure of a TF/FVIIa/XK1/10H10/nanodisc complex with a resolution of 3.7 Å, allowing us to model all the protein backbones. TF/FVIIa extends perpendicularly from the membrane, interacting with a "handle shaped" XK1 at two locations: the K1 domain docks into FVIIa's active site, while the γ-carboxyglutamate-rich (GLA) domain binds to TF's substrate-binding exosite. The FX and FVIIa GLA domains also contact each other and the membrane surface. Except for a minor contact between the first epidermal growth factor (EGF)-like domain of XK1 and TF, the rest of the FX light chain does not interact with TF/FVIIa. The structure reveals a previously unrecognized, membrane-dependent allosteric activation mechanism between FVIIa and TF where a serine-rich loop in TF that partially obscures the TF exosite must undergo a shift to allow access of the FX GLA domain to its final binding location on the membrane-bound TF/FVIIa complex. This mechanism also provides a novel explanation for the otherwise puzzling phenomenon of TF encryption/decryption on cell surfaces.
History
DepositionJun 9, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Downloads & links

-
Map

FileDownload / File: emd_71095.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNanodisc-embedded human TF/FVIIa/XK1 in complex with 10H10 Fab (3DFlex)
Voxel sizeX=Y=Z: 0.834 Å
Density
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.0076880623 - 0.016555093
Average (Standard dev.)0.000015753436 (±0.00028537476)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 350.28 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : Complex of factor VIIa, XK1 and the Fab fragment of antibody 10H1...

EntireName: Complex of factor VIIa, XK1 and the Fab fragment of antibody 10H10, all bound to tissue factor embedded in a nanodisc membrane bilayer.
Components
  • Complex: Complex of factor VIIa, XK1 and the Fab fragment of antibody 10H10, all bound to tissue factor embedded in a nanodisc membrane bilayer.
    • Complex: Human 10H10 antibody Fab
      • Protein or peptide: Human 10H10 antibody Fab heavy chain
      • Protein or peptide: Human 10H10 antibody Fab light chain
    • Complex: XK1 chimeric protein
      • Protein or peptide: Human factor X (FX) light chain
      • Protein or peptide: Human TFPI Kunitz domain 1 (K1)
    • Complex: Human activated FVIIa
      • Protein or peptide: Human factor VIIa - light chain
      • Protein or peptide: Human factor VIIa (FVIIa) protease domain
    • Complex: Human MBP-tagged tissue factor
      • Protein or peptide: Human tissue factor (TF)

+
Supramolecule #1: Complex of factor VIIa, XK1 and the Fab fragment of antibody 10H1...

SupramoleculeName: Complex of factor VIIa, XK1 and the Fab fragment of antibody 10H10, all bound to tissue factor embedded in a nanodisc membrane bilayer.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Map with nanodisc after 3D Flexible Refinement

+
Supramolecule #2: Human 10H10 antibody Fab

SupramoleculeName: Human 10H10 antibody Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #6-#7
Source (natural)Organism: Mus musculus (house mouse)

+
Supramolecule #3: XK1 chimeric protein

SupramoleculeName: XK1 chimeric protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #4: Human activated FVIIa

SupramoleculeName: Human activated FVIIa / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #5: Human MBP-tagged tissue factor

SupramoleculeName: Human MBP-tagged tissue factor / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: Human factor VIIa - light chain

MacromoleculeName: Human factor VIIa - light chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
ANAFL(CGU)(CGU)LRP GSL(CGU)R(CGU)CK(CGU)(CGU) QCSF(CGU)(CGU)AR(CGU)I FKDA(CGU)RTKLF

+
Macromolecule #2: Human factor VIIa (FVIIa) protease domain

MacromoleculeName: Human factor VIIa (FVIIa) protease domain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
IVGGKVCPKG ECPWQVLLLV NGAQLCGGTL INTIWVVSAA HCFDKIKNWR NLIAVLGEHD LSEHDGDEQS RRVAQVIIPS

+
Macromolecule #3: Human factor X (FX) light chain

MacromoleculeName: Human factor X (FX) light chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
ANSFL(CGU)(CGU)MKK GHL(CGU)R(CGU)CM(CGU)(CGU) TCSY(CGU)(CGU)AR(CGU)V F(CGU)DSDKTN

+
Macromolecule #4: Human TFPI Kunitz domain 1 (K1)

MacromoleculeName: Human TFPI Kunitz domain 1 (K1) / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
TDTELPPLKL MHSFCAFKAD DGPCKAIMKR FFFNIFTRQC EEFIYGGCEG NQNRFESLEE CKKMCTRD

+
Macromolecule #5: Human tissue factor (TF)

MacromoleculeName: Human tissue factor (TF) / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: TVAAYNLTWK STNFKTILEW EPKPVNQVYT VQISTKSGDW KSKCFYTTDT ECDLTDEIVK DVKQTYLARV FSYPAGNVES TGSAGEPLYE NSPEFTPYLE TNLGQPTIQS FEQVGTKVNV TVEDERTLVR RNNTFLSLRD VFGKDLIYTL YYWKSSSSGK KTAKTNTNEF ...String:
TVAAYNLTWK STNFKTILEW EPKPVNQVYT VQISTKSGDW KSKCFYTTDT ECDLTDEIVK DVKQTYLARV FSYPAGNVES TGSAGEPLYE NSPEFTPYLE TNLGQPTIQS FEQVGTKVNV TVEDERTLVR RNNTFLSLRD VFGKDLIYTL YYWKSSSSGK KTAKTNTNEF LIDVDKGENY CFSVQAVIPS RTVNRKSTDS PVECMGQEKG EFREIFYIIG AVVFVVIILV IILAISLHKG SGSGMKIEEG KLVIWINGDK GYNGLAEVGK KFEKDTGIKV TVEHPDKLEE KFPQVAATGD GPDIIFWAHD RFGGYAQSGL LAEITPDKAF QDKLYPFTWD AVRYNGKLIA YPIAVEALSL IYNKDLLPNP PKTWEEIPAL DKELKAKGKS ALMFNLQEPY FTWPLIAADG GYAFKYENGK YDIKDVGVDN AGAKAGLTFL VDLIKNKHMN ADTDYSIAEA AFNKGETAMT INGPWAWSNI DTSKVNYGVT VLPTFKGQPS KPFVGVLSAG INAASPNKEL AKEFLENYLL TDEGLEAVNK DKPLGAVALK SYEEELAKDP RIAATMENAQ KGEIMPNIPQ MSAFWYAVRT AVINAASGRQ TVDEALKDAQ T

+
Macromolecule #6: Human 10H10 antibody Fab heavy chain

MacromoleculeName: Human 10H10 antibody Fab heavy chain / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
SequenceString:
QVHLQQSGAE LMKPGASVKI SCKASGYTFI TYWIEWVKQR PGHGLEWIGD ILPGSGSTNY NENFKGKATF TADSSSNTAY

+
Macromolecule #7: Human 10H10 antibody Fab light chain

MacromoleculeName: Human 10H10 antibody Fab light chain / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
SequenceString:
DIVMTQSPSS LTVTAGEKVT MSCKSSQSLL SSGNQKNYLT WYQQIPGQPP KLLIYWASTR ESGVPDRFTG SGSGTDFTLT

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7132 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3440922
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Software - details: 3D Flex Refine
Details: 3D Flexible refinement with mesh created around the 10H10 antibody, the FVIIa/TF complex, the XK1 arm, and the membrane nanodisc.
Number images used: 91001
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

Initial modelPDB ID:

9p0x


Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: Model generated from associated entry

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more