2025-12-17 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID _em_admin.last_update RCSB RCSB 2025-06-07 2025-08-27 2025-08-27 2025-12-17 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 Director S10OD030275 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R24 GM145965 United States American Heart Association N028347 United States Photenhauer AL Sedzro JC Ohi MD Morrissey JH complex, nanodisc, blood clotting Sedzro JC Photenhauer AL Birkle F Meze K Mortenson A Duckworth C Wen PC Kearns S Cianfrocco MA Tajkhorshid E Ohi MD Morrissey JH Blood US 146 2833 2842 2025 40811856 doi:10.1182/blood.2025029430 1528-0020 9p0x FULLOVERLAP EMDB EMD-71090 associated EM volume

Nanodisc-embedded human TF/FVIIa/XK1 in complex with 10H10 Fab (nanodisc-subtracted)

Complex of factor VIIa, XK1 and the Fab fragment of antibody 10H10, all bound to tissue factor embedded in a nanodisc membrane bilayer. Complex of factor VIIa, XK1 and the Fab fragment of antibody 10H10, all bound to tissue factor embedded in a nanodisc membrane bilayer. 0 1 2 3 4 5 6 7

Map with nanodisc subtracted.

Human 10H10 antibody Fab 1 6 7 Mus musculus XK1 chimeric protein 1 2 5 Homo sapiens Human factor VIIa (FVIIa) 1 1 3 Homo sapiens Human MBP-tagged tissue factor 1 4 Homo sapiens Factor VII light chain Homo sapiens 0.016359772 1 Homo sapiens LEVO ANAFL(CGU)(CGU)LRPGSL(CGU)R(CGU)CK(CGU)(CGU)QCSF(CGU)(CGU)AR(CGU)IFKDA(CGU)RTKLF WISYSDGDQCASSPCQNGGSCKDQLQSYICFCLPAFEGRNCETHKDDQLICVNENGGCEQYCSDHTGTKRSCRCHEGYSL LADGVSCTPTVEYPCGKIPILE P08709 Factor X light chain Homo sapiens 0.015309423 1 Homo sapiens LEVO ANSFL(CGU)(CGU)MKKGHL(CGU)R(CGU)CM(CGU)(CGU)TCSY(CGU)(CGU)AR(CGU)VF(CGU)DSDKTN (CGU)FWNKYKDGDQCETSPCQNQGKCKDGLGEYTCTCLEGFEGKNCELFTRKLCSLDNGDCDQFCHEEQNSVVCSCARG YTLADNGKACIPTGPYP P00742 Coagulation factor VII Heavy Chain Homo sapiens 0.028103256 1 Homo sapiens LEVO IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHDLSEHDGDEQSRRVAQVIIPS TYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERTLAFVRFSLVSGWGQLLDRGATALELMVLNVPRLMTQDCLQ QSRKVGDSPNITEYMFCAGYSDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMR SEPRPGVLLRAPFP P08709 3.4.21.21 Tissue factor,Maltose/maltodextrin-binding periplasmic protein Escherichia coli 0.067828523 1 Escherichia coli BL21(DE3) LEVO TVAAYNLTWKSTNFKTILEWEPKPVNQVYTVQISTKSGDWKSKCFYTTDTECDLTDEIVKDVKQTYLARVFSYPAGNVES TGSAGEPLYENSPEFTPYLETNLGQPTIQSFEQVGTKVNVTVEDERTLVRRNNTFLSLRDVFGKDLIYTLYYWKSSSSGK KTAKTNTNEFLIDVDKGENYCFSVQAVIPSRTVNRKSTDSPVECMGQEKGEFREIFYIIGAVVFVVIILVIILAISLHKG SGSGMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGL LAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPY FTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNI DTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDP RIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQT P13726 P0AEY0 Tissue factor pathway inhibitor Homo sapiens 0.007979198 1 Homo sapiens LEVO TDTELPPLKLMHSFCAFKADDGPCKAIMKRFFFNIFTRQCEEFIYGGCEGNQNRFESLEECKKMCTRD P10646 Human 10H10 antibody Fab heavy chain Mus musculus BALB/c 0.023569252 1 LEVO QVHLQQSGAELMKPGASVKISCKASGYTFITYWIEWVKQRPGHGLEWIGDILPGSGSTNYNENFKGKATFTADSSSNTAY MQLSSLTSEDSAVYYCARSGYYGNSGFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVT WNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD Human 10H10 antibody Fab light chain Mus musculus BALB/c 0.024196708999999997 1 LEVO DIVMTQSPSSLTVTAGEKVTMSCKSSQSLLSSGNQKNYLTWYQQIPGQPPKLLIYWASTRESGVPDRFTGSGSGTDFTLT INSVQAEDLAVYYCQNDYTYPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSE RQNGVLNSATDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC MAGNESIUM ION 2.4305e-05 4 MG CALCIUM ION 4.0078e-05 12 CA beta-D-glucopyranose 0.000180156 1 BGC alpha-L-fucopyranose 0.000164156 1 FUC singleParticle particle 7.4 Quantifoil R2/2 COPPER 200 GLOW DISCHARGE 30 ETHANE 100 277 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 2.5 105000.0 20 GATAN K3 (6k x 4k) 1 7132 50.0 1 2862371 NONE C1 3.7 FSC 0.143 CUT-OFF cryoSPARC 20107 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD 1dan L 46-142 PDB experimental model 1dan H 16-257 PDB experimental model 1dan T 6-80 PDB experimental model 1dan U 91-210 PDB experimental model 3th2 L 1-46 PDB experimental model 1iod G 401-444 PDB experimental model 1xka L 49-139 PDB experimental model 4bqd A 12-79 PDB experimental model 12e8 H 112-214 PDB experimental model 12e8 L 107-214 PDB experimental model 4m7l H 1-119 PDB experimental model 4m7l L 1-113 PDB experimental model FLEXIBLE FIT

Crystal structures were rigid-body fit into the density map and model optimization was then carried out with Phenix real-space refine. Manual refinement in Coot was performed to ensure that the backbone traces followed the density in regions where the map was high enough resolution to trace the backbone. Secondary structure restraints were used to ensure that alpha-helices and beta-sheets did not deviate far from their expected geometry. A final check of MolProbity and cross correlation was done to ensure model quality.

cross-correlation REAL emd_71090_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 420 420 420 0 0 0 420 420 420 350.28 350.28 350.28 90.0 90.0 90.0 X Y Z -0.8588686 1.0776706 0.00014024475 0.08968307 0.834 0.834 0.834 AUTHOR ::::EMDATABANK.org::::EMD-71090:::: fVIIa/TF/XK1/10H10 half map B emd_71090_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 420 420 420 0 0 0 420 420 420 350.28 350.28 350.28 90.0 90.0 90.0 X Y Z -0.8149668 1.1626954 0.0001300412 0.09282095 0.834 0.834 0.834 AUTHOR ::::EMDATABANK.org::::EMD-71090:::: fVIIa/TF/XK1/10H10 half map A