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Entry
Database: EMDB / ID: EMD-74756
TitleStructural insights into the exosite-mediated activation of Factor IX by Factor XIa using cryoEM
Map dataDeepEMhancer sharpened map - using Binary mask - used for model building
Sample
  • Complex: Complex of Factor XIa (FXIa) with Factor IX (FIX).
    • Complex: Activated coagulation Factor XI (FXIa)
      • Protein or peptide: Coagulation factor XIa heavy chain
    • Complex: Coagulation Factor IX (FIX)
      • Protein or peptide: Coagulation factor IX
  • Protein or peptide: Coagulation factor XIa light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
KeywordsCoagulation / Intrinsic Pathway / Complex / Hemophilia / Factor IX / Factor XIa / BLOOD CLOTTING
Function / homology
Function and homology information


Defective F9 secretion / coagulation factor IXa / Defective gamma-carboxylation of F9 / coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX ...Defective F9 secretion / coagulation factor IXa / Defective gamma-carboxylation of F9 / coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / : / zymogen activation / plasminogen activation / Protein hydroxylation / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Removal of aminoterminal propeptides from gamma-carboxylated proteins / : / serine-type peptidase activity / Golgi lumen / blood coagulation / heparin binding / endopeptidase activity / extracellular matrix / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / proteolysis / : / extracellular exosome / extracellular region / membrane / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site ...Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Coagulation factor IX / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsMohammed BM
Funding support United States, 5 items
OrganizationGrant numberCountry
Other privateDoisy Fund of the Edward A. Doisy Department of Biochemistry and Molecular Biology
Childrens Discovery Institute of Washington University and St. Louis Childrens HospitalCDI-CORE-2015-505 and CDI-CORE-2019-813 United States
The Foundation for Barnes-Jewish Hospital3770 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK020579 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA091842 United States
CitationJournal: J Thromb Haemost / Year: 2026
Title: Structural insights into the exosite-mediated activation of Factor IX by Factor XIa using cryo-EM.
Authors: Bassem M Mohammed / Samantha Deavila / Tristan Friet / Isabella Dattilio /
Abstract: BACKGROUND: Factor XI (FXI) occupies a unique and clinically significant niche, bridging the tissue factor-driven and contact-driven coagulation pathways. Irrespective of the trigger, activated ...BACKGROUND: Factor XI (FXI) occupies a unique and clinically significant niche, bridging the tissue factor-driven and contact-driven coagulation pathways. Irrespective of the trigger, activated factor XI (FXIa) contributes to clotting by activating factor IX (FIX). Biochemical studies established that this reaction requires the membrane-binding FIX-Gla domain to engage an exosite on the FXIa Apple 3 (A3) domain, that only become available upon FXI activation. Structural data for FXIa, FIX, FIXaβ, and the FXIa:FIX complex are lacking; current understanding relies on zymogen FXI crystal structures and homology modeling of FXIa after kallikrein.
OBJECTIVES: Elucidate the high-resolution structure of FXIa in functionally relevant conformation in complex with FIX.
METHODS: We utilized cryogenic electron microscopy (cryo-EM) to determine the structures of human FXIa in complex with its full-length substrate, FIX, and activated product, FIXaβ.
RESULTS: We report the first cryo-EM structures of FXIa in complex with its substrate, FIX, and activated FIX (FIXaβ). The structures capture a functionally relevant conformational change in the ...RESULTS: We report the first cryo-EM structures of FXIa in complex with its substrate, FIX, and activated FIX (FIXaβ). The structures capture a functionally relevant conformational change in the FXIa catalytic domain and reveals the first view of the entire FIX and FIXaβ. Critically, we visualize the FIX-Gla domain precisely docked to the FXIa-A3 exosite on both subunits of the FXIa dimer. We also define the first step of proteolysis, visualizing the FIX Arg145 inserted into the primary specificity pocket of FXIa.
CONCLUSIONS: The structures define the full FXIa:FIX interface providing a structural template for understanding the sequential activation of FIX and for developing a new class of selective ...CONCLUSIONS: The structures define the full FXIa:FIX interface providing a structural template for understanding the sequential activation of FIX and for developing a new class of selective allosteric antithrombotic agents.
History
DepositionDec 23, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74756.png

Downloads & links

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Map

FileDownload / File: emd_74756.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer sharpened map - using Binary mask - used for model building
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 416 pix.
= 386.048 Å		0.93 Å/pix.
x 416 pix.
= 386.048 Å		0.93 Å/pix.
x 416 pix.
= 386.048 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.928 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.226
Minimum - Maximum-0.000828081 - 2.5183291
Average (Standard dev.)0.00079178426 (±0.021641571)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 386.04797 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74756_msk_1.map
Projections & Slices
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Additional map: DeepEMhanccer sharpened map - widetarget

Fileemd_74756_additional_1.map
AnnotationDeepEMhanccer sharpened map - widetarget
Projections & Slices
AxesZYX

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Histogram

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Additional map: Unsharpened local refined map for Class1 volume

Fileemd_74756_additional_2.map
AnnotationUnsharpened local refined map for Class1 volume
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_74756_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_74756_half_map_2.map
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Sample components

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Entire : Complex of Factor XIa (FXIa) with Factor IX (FIX).

EntireName: Complex of Factor XIa (FXIa) with Factor IX (FIX).
Components
  • Complex: Complex of Factor XIa (FXIa) with Factor IX (FIX).
    • Complex: Activated coagulation Factor XI (FXIa)
      • Protein or peptide: Coagulation factor XIa heavy chain
    • Complex: Coagulation Factor IX (FIX)
      • Protein or peptide: Coagulation factor IX
  • Protein or peptide: Coagulation factor XIa light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: Complex of Factor XIa (FXIa) with Factor IX (FIX).

SupramoleculeName: Complex of Factor XIa (FXIa) with Factor IX (FIX). / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3
Details: FXIa is a dimer and binds 2 FIX molecules. Factor XIa used in this preparation is recombinant FXIa with a Ser557Ala mutation (mature protein numbering). recombinant protein is made as a ...Details: FXIa is a dimer and binds 2 FIX molecules. Factor XIa used in this preparation is recombinant FXIa with a Ser557Ala mutation (mature protein numbering). recombinant protein is made as a zymogen that is activated. The activation involve cleavage after residue Arg369 of FXI to give FXIa
Source (natural)Organism: Homo sapiens (human) / Organ: liver / Tissue: Plasma
Molecular weightTheoretical: 57 KDa

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Supramolecule #2: Activated coagulation Factor XI (FXIa)

SupramoleculeName: Activated coagulation Factor XI (FXIa) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: Made from recombinant FXI that was activated to give FXIa. Has a Ser557Ala mutation to render it catalytically dead.
Source (natural)Organism: Homo sapiens (human) / Organ: liver / Tissue: Plasma

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Supramolecule #3: Coagulation Factor IX (FIX)

SupramoleculeName: Coagulation Factor IX (FIX) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 / Details: Purified from human plasma
Source (natural)Organism: Homo sapiens (human) / Organ: liver / Tissue: Plasma

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Macromolecule #1: Coagulation factor XIa heavy chain

MacromoleculeName: Coagulation factor XIa heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: coagulation factor XIa
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.262098 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ECVTQLLKDT CFEGGDITTV FTPSAKYCQV VCTYHPRCLL FTFTAESPSE DPTRWFTCVL KDSVTETLPR VNRTAAISGY SFKQCSHQI SACNKDIYVD LDMKGINYNS SVAKSAQECQ ERCTDDVHCH FFTYATRQFP SLEHRNICLL KHTQTGTPTR I TKLDKVVS ...String:
ECVTQLLKDT CFEGGDITTV FTPSAKYCQV VCTYHPRCLL FTFTAESPSE DPTRWFTCVL KDSVTETLPR VNRTAAISGY SFKQCSHQI SACNKDIYVD LDMKGINYNS SVAKSAQECQ ERCTDDVHCH FFTYATRQFP SLEHRNICLL KHTQTGTPTR I TKLDKVVS GFSLKSCALS NLACIRDIFP NTVFADSNID SVMAPDAFVC GRICTHHPGC LFFTFFSQEW PKESQRNLCL LK TSESGLP STRIKKSKAL SGFSLQSCRH SIPVFCHSSF YHDTDFLGEE LDIVAAKSHE ACQKLCTNAV RCQFFTYTPA QAS CNEGKG KCYLKLSSNG SPTKILHGRG GISGYTLRLC KMDNECTTKI KPR

UniProtKB: Coagulation factor XI

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Macromolecule #2: Coagulation factor XIa light chain

MacromoleculeName: Coagulation factor XIa light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.686352 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IVGGTASVRG EWPWQVTLHT TSPTQRHLCG GSIIGNQWIL TAAHCFYGVE SPKILRVYSG ILNQSEIKED TSFFGVQEII IHDQYKMAE SGYDIALLKL ETTVNYTDSQ RPICLPSKGD RNVIYTDCWV TGWGYRKLRD KIQNTLQKAK IPLVTNEECQ K RYRGHKIT ...String:
IVGGTASVRG EWPWQVTLHT TSPTQRHLCG GSIIGNQWIL TAAHCFYGVE SPKILRVYSG ILNQSEIKED TSFFGVQEII IHDQYKMAE SGYDIALLKL ETTVNYTDSQ RPICLPSKGD RNVIYTDCWV TGWGYRKLRD KIQNTLQKAK IPLVTNEECQ K RYRGHKIT HKMICAGYRE GGKDACKGDA GGPLSCKHNE VWHLVGITSW GEGCAQRERP GVYTNVVEYV DWILEKTQ

UniProtKB: Coagulation factor XI

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Macromolecule #3: Coagulation factor IX

MacromoleculeName: Coagulation factor IX / type: protein_or_peptide / ID: 3
Details: CGU are Glu residues with post-translational modification adding a carboxyl group to the gamma carbon of Glu
Number of copies: 1 / Enantiomer: LEVO / EC number: coagulation factor IXa
Source (natural)Organism: Homo sapiens (human) / Tissue: plasma
Molecular weightTheoretical: 47.158219 KDa
SequenceString: YNSGKL(CGU)(CGU)FV QGNL(CGU)R(CGU)CM(CGU) (CGU)KCSF(CGU)(CGU)AR(CGU) VF(CGU)NT(CGU) RTT (CGU)FWKQYVDGD QCESNPCLNG GSCKDDINSY ECWCPFGFEG KNCELDVTCN IKNGRCEQFC KNSADNKVVC SCT EGYRLA ENQKSCEPAV ...String:
YNSGKL(CGU)(CGU)FV QGNL(CGU)R(CGU)CM(CGU) (CGU)KCSF(CGU)(CGU)AR(CGU) VF(CGU)NT(CGU) RTT (CGU)FWKQYVDGD QCESNPCLNG GSCKDDINSY ECWCPFGFEG KNCELDVTCN IKNGRCEQFC KNSADNKVVC SCT EGYRLA ENQKSCEPAV PFPCGRVSVS QTSKLTRAET VFPDVDYVNS TEAETILDNI TQSTQSFNDF TRVVGGEDAK PGQF PWQVV LNGKVDAFCG GSIVNEKWIV TAAHCVETGV KITVVAGEHN IEETEHTEQK RNVIRIIPHH NYNAAINKYN HDIAL LELD EPLVLNSYVT PICIADKEYT NIFLKFGSGY VSGWGRVFHK GRSALVLQYL RVPLVDRATC LRSTKFTIYN NMFCAG FHE GGRDSCQGDS GGPHVTEVEG TSFLTGIISW GEECAMKGKY GIYTKVSRYV NWIKEKTKLT

UniProtKB: Coagulation factor IX

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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: 4 / 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: 7 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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 #1

Preparation ID1
Concentration0.1 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMSodium ChlorideNaCl
5.0 mMCalcium chlorideCaCl2
GridModel: Quantifoil R1.2/1.3 / Support film - Film type ID: 1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Sample preparation #2

Preparation ID2
Concentration0.1 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMSodium ChlorideNaCl
5.0 mMCalcium chlorideCaCl2
GridModel: Quantifoil R1.2/1.3 / Support film - Film type ID: 1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON IV (4k x 4k) / #0 - Digitization - Dimensions - Width: 4096 pixel / #0 - Digitization - Dimensions - Height: 4096 pixel / #0 - Number grids imaged: 1 / #0 - Number real images: 4662 / #0 - Average electron dose: 60.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON IV (4k x 4k) / #1 - Digitization - Dimensions - Width: 4096 pixel / #1 - Digitization - Dimensions - Height: 4096 pixel / #1 - Number grids imaged: 1 / #1 - Number real images: 1832 / #1 - Average electron dose: 57.2 e/Å2 / #1 - Details: 30 degree tilt / #2 - Image recording ID: 3 / #2 - Film or detector model: FEI FALCON IV (4k x 4k) / #2 - Digitization - Dimensions - Width: 4096 pixel / #2 - Digitization - Dimensions - Height: 4096 pixel / #2 - Number grids imaged: 1 / #2 - Number real images: 1297 / #2 - Average electron dose: 52.5 e/Å2 / #3 - Image recording ID: 4 / #3 - Film or detector model: FEI FALCON IV (4k x 4k) / #3 - Digitization - Dimensions - Width: 4096 pixel / #3 - Digitization - Dimensions - Height: 4096 pixel / #3 - Number grids imaged: 1 / #3 - Number real images: 817 / #3 - Average electron dose: 52.5 e/Å2 / #4 - Image recording ID: 5 / #4 - Film or detector model: FEI FALCON IV (4k x 4k) / #4 - Digitization - Dimensions - Width: 4096 pixel / #4 - Digitization - Dimensions - Height: 4096 pixel / #4 - Number grids imaged: 1 / #4 - Number real images: 2789 / #4 - Average electron dose: 50.0 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: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 150000
Sample stageCooling holder cryogen: NITROGEN

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Image processing #1

Image processing ID1
Image recording ID1
Particle selectionNumber selected: 682170
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup model#0 - Type of model: NONE / #1 - Type of model: NONE / #2 - Type of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 103693
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.7.1)
FSC plot (resolution estimation)

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Image processing #2

Image processing ID2
Image recording ID2
Particle selectionNumber selected: 682170
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup model#0 - Type of model: NONE / #1 - Type of model: NONE / #2 - Type of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 103693
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.7.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

6i58

source_name: PDB, initial_model_type: experimental modelFactor XI

1nl0

source_name: PDB, initial_model_type: experimental modelFactor IX - Gla

1-v4

source_name: AlphaFold, initial_model_type: in silico modelFactor IX

9zqy

source_name: PDB, initial_model_type: experimental modelRelated entry to this deposition built by ab-initio
DetailsCombined Rigid fit, backbone trace, and ab-initio
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-9ztk:
Structural insights into the exosite-mediated activation of Factor IX by Factor XIa using cryoEM

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