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Entry
Database: EMDB / ID: EMD-74894
TitleStructural insights into the exosite-mediated activation of Factor IX by Factor XIa using cryoEM
Map dataDeepEMhancer sharpened composite map
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
      • Protein or peptide: Coagulation factor XIa light chain
    • Complex: Coagulation Factor IX (FIX)
      • Protein or peptide: Coagulation factor IXa light chain
      • Protein or peptide: Coagulation factor IXa heavy 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: 3.4 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 United States
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 31, 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_74894.png

Downloads & links

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Map

FileDownload / File: emd_74894.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer sharpened composite map
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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.928 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0534
Minimum - Maximum-0.0018245871 - 2.4912581
Average (Standard dev.)0.00048393087 (±0.01691506)
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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Additional map: Unsharpened - composite map

Fileemd_74894_additional_1.map
AnnotationUnsharpened - composite 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 : 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
      • Protein or peptide: Coagulation factor XIa light chain
    • Complex: Coagulation Factor IX (FIX)
      • Protein or peptide: Coagulation factor IXa light chain
      • Protein or peptide: Coagulation factor IXa heavy 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: #1-#4
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 involves cleavage after residue Arg369 of FXI to give FXIa
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-#2
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-#4 / 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
Details: Activated Recombinant Factor XI Ser557Ala. The molecule is a dimer that is disulphide linked at Cys321. During activation the bond at R369 is cleaved on each subunit to give a two chain ...Details: Activated Recombinant Factor XI Ser557Ala. The molecule is a dimer that is disulphide linked at Cys321. During activation the bond at R369 is cleaved on each subunit to give a two chain molecule. only one monomer is solved here and is composed of a heavy chain (A) and light (B)
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
Details: Activated Recombinant Factor XI Ser557Ala. The molecule is a dimer that is disulphide linked at Cys321. During activation the bond at R369 is cleaved on each subunit to give a two chain ...Details: Activated Recombinant Factor XI Ser557Ala. The molecule is a dimer that is disulphide linked at Cys321. During activation the bond at R369 is cleaved on each subunit to give a two chain molecule. only one monomer is solved here and is composed of a heavy chain (A) and light (B)
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 IXa light chain

MacromoleculeName: Coagulation factor IXa light chain / 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
Source (natural)Organism: Homo sapiens (human) / Tissue: plasma
Molecular weightTheoretical: 17.033383 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 PFPCGRVSVS QTSKLTR

UniProtKB: Coagulation factor IX

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Macromolecule #4: Coagulation factor IXa heavy chain

MacromoleculeName: Coagulation factor IXa heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: coagulation factor IXa
Source (natural)Organism: Homo sapiens (human) / Tissue: plasma
Molecular weightTheoretical: 26.190818 KDa
SequenceString: VVGGEDAKPG QFPWQVVLNG KVDAFCGGSI VNEKWIVTAA HCVETGVKIT VVAGEHNIEE TEHTEQKRNV IRIIPHHNYN AAINKYNHD IALLELDEPL VLNSYVTPIC IADKEYTNIF LKFGSGYVSG WGRVFHKGRS ALVLQYLRVP LVDRATCLRS T KFTIYNNM ...String:
VVGGEDAKPG QFPWQVVLNG KVDAFCGGSI VNEKWIVTAA HCVETGVKIT VVAGEHNIEE TEHTEQKRNV IRIIPHHNYN AAINKYNHD IALLELDEPL VLNSYVTPIC IADKEYTNIF LKFGSGYVSG WGRVFHKGRS ALVLQYLRVP LVDRATCLRS T KFTIYNNM FCAGFHEGGR DSCQGDSGGP HVTEVEGTSF LTGIISWGEE CAMKGKYGIY TKVSRYVNWI KEKTKLT

UniProtKB: Coagulation factor IX

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / 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 #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 8 / 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 / Material: COPPER / Mesh: 300 / 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 / Material: COPPER / Mesh: 300 / 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 224103
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.7.1)

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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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 224103
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.7.1)

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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 backbone trace, and ab-initio
RefinementSpace: REAL / Protocol: OTHER
Output model

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

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