Structure of the Complement classical and lectin pathway proconvertase, C4b2

2026-03-04 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY 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.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.identifier_ORCID _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.identifier_ORCID _em_admin.last_update PDBe PDBe 2025-03-18 2025-12-24 2025-12-24 2026-03-04 Consejo Nacional de Ciencia y Tecnologia (CONACYT) CVU 604718 Mexico Netherlands Organisation for Scientific Research (NWO) 01.80.104.00 Netherlands European Research Council (ERC) 787241 European Union Structure of the Complement classical and lectin pathway proconvertase, C4b2 De la O Becerra KI Brondijk THC Gros P Proconvertase, Complement, classical pathway, C4b2, IMMUNE SYSTEM De la O Becerra KI Brondijk THC Serna Martin I Gros P Structural insights into C3 convertase activity of the classical pathway of complement. Nat Commun UK 17 993 993 2025 41413058 doi:10.1038/s41467-025-67730-4 2041-1723 9qj5 FULLOVERLAP EMDB EMD-53199 associated EM volume

PDB 9QJ4 unspecified

structure C4b2

PDB 9QPY unspecified

structure C4b2b

PDB 9QK2 unspecified

structure C4b2bC3

Classical and lectin pathway C3 proconvertase Classical and lectin pathway C3 proconvertase 0 1 2 Homo sapiens blood plasma 0.288 Complement C4-A Homo sapiens blood plasma 0.193007234 3 LEVO MRLLWGLIWASSFFTLSLQKPRLLLFSPSVVHLGVPLSVGVQLQDVPRGQVVKGSVFLRNPSRNNVPCSPKVDFTLSSER DFALLSLQVPLKDAKSCGLHQLLRGPEVQLVAHSPWLKDSLSRTTNIQGINLLFSSRRGHLFLQTDQPIYNPGQRVRYRV FALDQKMRPSTDTITVMVENSHGLRVRKKEVYMPSSIFQDDFVIPDISEPGTWKISARFSDGLESNSSTQFEVKKYVLPN FEVKITPGKPYILTVPGHLDEMQLDIQARYIYGKPVQGVAYVRFGLLDEDGKKTFFRGLESQTKLVNGQSHISLSKAEFQ DALEKLNMGITDLQGLRLYVAAAIIESPGGEMEEAELTSWYFVSSPFSLDLSKTKRHLVPGAPFLLQALVREMSGSPASG IPVKVSATVSSPGSVPEVQDIQQNTDGSGQVSIPIIIPQTISELQLSVSAGSPHPAIARLTVAAPPSGGPGFLSIERPDS RPPRVGDTLNLNLRAVGSGATFSHYYYMILSRGQIVFMNREPKRTLTSVSVFVDHHLAPSFYFVAFYYHGDHPVANSLRV DVQAGACEGKLELSVDGAKQYRNGESVKLHLETDSLALVALGALDTALYAAGSKSHKPLNMGKVFEAMNSYDLGCGPGGG DSALQVFQAAGLAFSDGDQWTLSRKRLSCPKEKTTRKKRNVNFQKAINEKLGQYASPTAKRCCQDGVTRLPMMRSCEQRA ARVQQPDCREPFLSCCQFAESLRKKSRDKGQAGLQRALEILQEEDLIDEDDIPVRSFFPENWLWRVETVDRFQILTLWLP DSLTTWEIHGLSLSKTKGLCVATPVQLRVFREFHLHLRLPMSVRRFEQLELRPVLYNYLDKNLTVSVHVSPVEGLCLAGG GGLAQQVLVPAGSARPVAFSVVPTAAAAVSLKVVARGSFEFPVGDAVSKVLQIEKEGAIHREELVYELNPLDHRGRTLEI PGNSDPNMIPDGDFNSYVRVTASDPLDTLGSEGALSPGGVASLLRLPRGCGEQTMIYLAPTLAASRYLDKTEQWSTLPPE TKDHAVDLIQKGYMRIQQFRKADGSYAAWLSRDSSTWLTAFVLKVLSLAQEQVGGSPEKLQETSNWLLSQQQADGSFQDP CPVLDRSMQGGLVGNDETVALTAFVTIALHHGLAVFQDEGAEPLKQRVEASISKANSFLGEKASAGLLGAHAAAITAYAL TLTKAPVDLLGVAHNNLMAMAQETGDNLYWGSVTGSQSNAVSPTPAPRNPSDPMPQAPALWIETTAYALLHLLLHEGKAE MADQASAWLTRQGSFQGGFRSTQDTVIALDALSAYWIASHTTEERGLNVTLSSTGRNGFKSHALQLNNRQIRGLEEELQF SLGSKINVKVGGNSKGTLKVLRTYNVLDMKNTTCQDLQIEVTVKGHVEYTMEANEDYEDYEYDELPAKDDPDAPLQPVTP LQLFEGRRNRRRREAPKVVEEQESRVHYTVCIWRNGKVGLSGMAIADVTLLSGFHALRADLEKLTSLSDRYVSHFETEGP HVLLYFDSVPTSRECVGFEAVQEVPVGLVQPASATLYDYYNPERRCSVFYGAPSKSRLLATLCSAEVCQCAEGKCPRQRR ALERGLQDEDGYRMKFACYYPRVEYGFQVKVLREDSRAAFRLFETKITQVLHFTKDVKAAANQMRNFLVRASCRLRLEPG KEYLIMGLDGATYDLEGHPQYLLDSNSWIEEMPSERLCRSTRQRAACAQLNDFLQEYGTQGCQV P0C0L4 Complement C2 Homo sapiens blood plasma 0.083363766 1 LEVO MGPLMVLFCLLFLYPGLADSAPSCPQNVNISGGTFTLSHGWAPGSLLTYSCPQGLYPSPASRLCKSSGQWQTPGATRSLS KAVCKPVRCPAPVSFENGIYTPRLGSYPVGGNVSFECEDGFILRGSPVRQCRPNGMWDGETAVCDNGAGHCPNPGISLGA VRTGFRFGHGDKVRYRCSSNLVLTGSSERECQGNGVWSGTEPICRQPYSYDFPEDVAPALGTSFSHMLGATNPTQKTKES LGRKIQIQRSGHLNLYLLLDCSQSVSENDFLIFKESASLMVDRIFSFEINVSVAIITFASEPKVLMSVLNDNSRDMTEVI SSLENANYKDHENGTGTNTYAALNSVYLMMNNQMRLLGMETMAWQEIRHAIILLTDGKSNMGGSPKTAVDHIREILNINQ KRNDYLDIYAIGVGKLDVDWRELNELGSKKDGERHAFILQDTKALHQVFEHMLDVSKLTDTICGVGNMSANASDQERTPW HVTIKPKSQETCRGALISDQWVLTAAHCFRDGNDHSLWRVNVGDPKSQWGKEFLIEKAVISPGFDVFAKKNQGILEFYGD DIALLKLAQKVKMSTHARPICLPCTMEANLALRRPQGSTCRDHENELLNKQSVPAHFVALNGSKLNINLKMGVEWTSCAE VVSQEKTMFPNLTDVREVVTDQFLCSGTQEDESPCKGESGGAVFLERRFRFFQVGLVSWGLYNPCLGSADKNSRKRAPRS KVPPPRDFHINLFRMQPWLRQHLGDVLNFLPL P06681 3.4.21.43 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 3 NAG MAGNESIUM ION 2.4305e-05 1 MG singleParticle particle 0.2 7.4 150.0 NaCl sodium chloride 20.0 HEPES 2.0 MgCl2 Magnesium chloride Quantifoil R1.2/1.3 GOLD 200 CARBON HOLEY GLOW DISCHARGE 30 ETHANE 95 277 FEI VITROBOT MARK IV

Complex was crosslinked with glutaraldehyde 0.2%

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.0 2.2 105000.0 NITROGEN GATAN K3 (6k x 4k) 1 4662 2.24 50.0 1 2647189 cryoSPARC v3.2/3 NONE 1 C1 FOURIER SPACE 3.5 FSC 0.143 CUT-OFF cryoSPARC v3.2/3 112621 MAXIMUM LIKELIHOOD cryoSPARC v3.2/3 MAXIMUM LIKELIHOOD cryoSPARC v3.2/3 cryoSPARC v3.2/3 emd_53199.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 401.28 401.28 401.28 90.0 90.0 90.0 X Y Z -0.8327031 1.2203819 -0.00018197171 0.016503796 0.836 0.836 0.836 0.12 AUTHOR ::::EMDATABANK.org::::EMD-53199:::: Sharpened map of Complement C4b in complex with C2 5JTW A PDB experimental model 5JTW B PDB experimental model 5JTW C PDB experimental model 3ERB D 1-235 PDB experimental model 2I6Q D 240-752 PDB experimental model FLEXIBLE FIT REAL emd_53199_msk_1.map emd_53199_msk_2.map emd_53199_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 401.28 401.28 401.28 90.0 90.0 90.0 X Y Z -0.20817828 0.4718979 -0.0001819717 0.008339765 0.836 0.836 0.836 AUTHOR ::::EMDATABANK.org::::EMD-53199:::: Unsharpened map of Complement C4b in complex with C2 emd_53199_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 401.28 401.28 401.28 90.0 90.0 90.0 X Y Z 0.0 52.060516 0.09354055 0.8038115 0.836 0.836 0.836 AUTHOR ::::EMDATABANK.org::::EMD-53199:::: Local resolution map of Complement C4b in complex with C2 emd_53199_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 401.28 401.28 401.28 90.0 90.0 90.0 X Y Z -0.34889776 0.6458357 0.00011079339 0.03427477 0.836 0.836 0.836 AUTHOR ::::EMDATABANK.org::::EMD-53199:::: Half map B of Complement C4b in complex with C2 emd_53199_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 401.28 401.28 401.28 90.0 90.0 90.0 X Y Z -0.39854488 0.6662488 0.000115175375 0.034625936 0.836 0.836 0.836 AUTHOR ::::EMDATABANK.org::::EMD-53199:::: Half map A of Complement C4b in complex with C2