Structural insights into the exosite-mediated activation of Factor IX by Factor XIa using cryoEM

2026-09-09 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY RCSB RCSB 2025-12-23 2026-09-09 2026-09-09 2026-09-09 Other private Doisy Fund of the Edward A. Doisy Department of Biochemistry and Molecular Biology Childrens Discovery Institute of Washington University and St. Louis Childrens Hospital CDI-CORE-2015-505 and CDI-CORE-2019-813 United States The Foundation for Barnes-Jewish Hospital 3770 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 Structural insights into the exosite-mediated activation of Factor IX by Factor XIa using cryoEM Mohammed BM Coagulation, Intrinsic Pathway, Complex, Hemophilia, Factor IX, Factor XIa, BLOOD CLOTTING Mohammed BM Deavila S Friet T Dattilio I Structural insights into the exosite-mediated activation of Factor IX by Factor XIa using cryo-EM. J.Thromb.Haemost. UK 2026 42628751 doi:10.1016/j.jtha.2026.08.015 1538-7836 EMD-74584 focused EM volume 9ztk FULLOVERLAP PDB 9ZQY unspecified

Model that goes with EMD-74584

EMDB EMD-74584 focused EM volume EMDB EMD-74756 associated EM volume

Complex of Factor XIa (FXIa) with Factor IX (FIX). Complex of Factor XIa (FXIa) with Factor IX (FIX). 0 3

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

Homo sapiens liver Plasma 0.057 Activated coagulation Factor XI (FXIa) 1 1

Made from recombinant FXI that was activated to give FXIa. Has a Ser557Ala mutation to render it catalytically dead.

Homo sapiens liver Plasma Coagulation Factor IX (FIX) 1 3

Purified from human plasma

Homo sapiens liver Plasma Coagulation factor XIa heavy chain Homo sapiens 0.041262098 1 Homo sapiens LEVO ECVTQLLKDTCFEGGDITTVFTPSAKYCQVVCTYHPRCLLFTFTAESPSEDPTRWFTCVLKDSVTETLPRVNRTAAISGY SFKQCSHQISACNKDIYVDLDMKGINYNSSVAKSAQECQERCTDDVHCHFFTYATRQFPSLEHRNICLLKHTQTGTPTRI TKLDKVVSGFSLKSCALSNLACIRDIFPNTVFADSNIDSVMAPDAFVCGRICTHHPGCLFFTFFSQEWPKESQRNLCLLK TSESGLPSTRIKKSKALSGFSLQSCRHSIPVFCHSSFYHDTDFLGEELDIVAAKSHEACQKLCTNAVRCQFFTYTPAQAS CNEGKGKCYLKLSSNGSPTKILHGRGGISGYTLRLCKMDNECTTKIKPR P03951 3.4.21.27 Coagulation factor XIa light chain Homo sapiens 0.026686351999999997 1 Homo sapiens LEVO IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEII IHDQYKMAESGYDIALLKLETTVNYTDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQK RYRGHKITHKMICAGYREGGKDACKGDAGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQ P03951 Coagulation factor IX Homo sapiens plasma 0.047158218999999994

CGU are Glu residues with post-translational modification adding a carboxyl group to the gamma carbon of Glu

1 LEVO YNSGKL(CGU)(CGU)FVQGNL(CGU)R(CGU)CM(CGU)(CGU)KCSF(CGU)(CGU)AR(CGU)VF(CGU)NT(CGU) RTT(CGU)FWKQYVDGDQCESNPCLNGGSCKDDINSYECWCPFGFEGKNCELDVTCNIKNGRCEQFCKNSADNKVVCSCT EGYRLAENQKSCEPAVPFPCGRVSVSQTSKLTRAETVFPDVDYVNSTEAETILDNITQSTQSFNDFTRVVGGEDAKPGQF PWQVVLNGKVDAFCGGSIVNEKWIVTAAHCVETGVKITVVAGEHNIEETEHTEQKRNVIRIIPHHNYNAAINKYNHDIAL LELDEPLVLNSYVTPICIADKEYTNIFLKFGSGYVSGWGRVFHKGRSALVLQYLRVPLVDRATCLRSTKFTIYNNMFCAG FHEGGRDSCQGDSGGPHVTEVEGTSFLTGIISWGEECAMKGKYGIYTKVSRYVNWIKEKTKLT P00740 3.4.21.22 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 4 NAG CALCIUM ION 4.0078e-05 7 CA singleParticle particle 0.1 7.4 20.0 HEPES 150.0 NaCl Sodium Chloride 5.0 CaCl2 Calcium chloride Quantifoil R1.2/1.3 CARBON HOLEY GLOW DISCHARGE 20 AIR ETHANE 95 277.15 FEI VITROBOT MARK IV 0.1 7.4 20.0 HEPES 150.0 NaCl Sodium Chloride 5.0 CaCl2 Calcium chloride Quantifoil R1.2/1.3 CARBON HOLEY GLOW DISCHARGE 20 AIR ETHANE 95 277.15 FEI VITROBOT MARK IV TFS GLACIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.7 1.0 2.4 150000.0 NITROGEN FEI FALCON IV (4k x 4k) 4096 4096 1 4662 60.0 FEI FALCON IV (4k x 4k) 4096 4096 1 1832 57.2

30 degree tilt

FEI FALCON IV (4k x 4k) 4096 4096 1 1297 52.5 FEI FALCON IV (4k x 4k) 4096 4096 1 817 52.5 FEI FALCON IV (4k x 4k) 4096 4096 1 2789 50.0 1 682170 cryoSPARC 4.7.1 PHASE FLIPPING AND AMPLITUDE CORRECTION 1 C1 BACK PROJECTION 3.7 FSC 0.143 CUT-OFF cryoSPARC 4.7.1 103693 NOT APPLICABLE NOT APPLICABLE 3 cryoSPARC 4.7.1 2 682170 cryoSPARC 4.7.1 PHASE FLIPPING AND AMPLITUDE CORRECTION 1 BACK PROJECTION 3.7 FSC 0.143 CUT-OFF cryoSPARC 4.7.1 103693 NOT APPLICABLE NOT APPLICABLE 3 cryoSPARC 4.7.1 emd_74756.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 386.04797 386.04797 386.04797 90.0 90.0 90.0 X Y Z -0.000828081 2.5183291 0.00079178426 0.021641571 0.9279999 0.9279999 0.9279999 0.226 AUTHOR ::::EMDATABANK.org::::EMD-74756:::: DeepEMhancer sharpened map - using Binary mask - used for model building 6I58 PDB experimental model

Factor XI

1NL0 PDB experimental model

Factor IX - Gla

AF-F2RM35-F1-v4 AlphaFold in silico model

Factor IX

9ZqY PDB experimental model

Related entry to this deposition built by ab-initio

OTHER

Combined Rigid fit, backbone trace, and ab-initio

REAL emd_74756_msk_1.map emd_74756_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 386.04797 386.04797 386.04797 90.0 90.0 90.0 X Y Z -0.7688093 1.9005716 -0.00009394659 0.025910834 0.9279999 0.9279999 0.9279999 AUTHOR ::::EMDATABANK.org::::EMD-74756:::: Unsharpened local refined map for Class1 volume emd_74756_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 386.04797 386.04797 386.04797 90.0 90.0 90.0 X Y Z -0.004570959 2.2071733 0.0006361123 0.01709555 0.9279999 0.9279999 0.9279999 AUTHOR ::::EMDATABANK.org::::EMD-74756:::: DeepEMhanccer sharpened map - widetarget emd_74756_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 386.04797 386.04797 386.04797 90.0 90.0 90.0 X Y Z -1.1794657 2.1705225 0.00047520816 0.07849786 0.9279999 0.9279999 0.9279999 AUTHOR ::::EMDATABANK.org::::EMD-74756:::: emd_74756_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 386.04797 386.04797 386.04797 90.0 90.0 90.0 X Y Z -1.1660877 2.4594982 0.0004650047 0.07856369 0.9279999 0.9279999 0.9279999 AUTHOR ::::EMDATABANK.org::::EMD-74756::::