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- EMDB-63894: CP/MBL pathways C3 convertase C4b2a and C3 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63894
TitleCP/MBL pathways C3 convertase C4b2a and C3 complex
Map data
Sample
  • Complex: CP/MBL pathways C3 convertases C4b2a and C3 complex
    • Protein or peptide: Serine protease complement C2b
    • Protein or peptide: Complement C3
    • Protein or peptide: Complement C4-B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: NICKEL (II) ION
KeywordsCP/MBL pathways / C3 convertases and substrate / C4b2a_C3 complex / IMMUNE SYSTEM
Function / homology
Function and homology information


classical-complement-pathway C3/C5 convertase / detection of molecule of bacterial origin / symbiont cell surface / opsonization / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / complement binding / positive regulation of activation of membrane attack complex / response to thyroid hormone ...classical-complement-pathway C3/C5 convertase / detection of molecule of bacterial origin / symbiont cell surface / opsonization / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / complement binding / positive regulation of activation of membrane attack complex / response to thyroid hormone / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of phagocytosis, engulfment / Activation of C3 and C5 / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of type IIa hypersensitivity / complement receptor mediated signaling pathway / complement-dependent cytotoxicity / positive regulation of D-glucose transmembrane transport / complement activation / complement activation, alternative pathway / endopeptidase inhibitor activity / Initial triggering of complement / neuron remodeling / amyloid-beta clearance / B cell activation / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / Purinergic signaling in leishmaniasis infection / response to nutrient / Peptide ligand-binding receptors / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / fatty acid metabolic process / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of protein phosphorylation / azurophil granule lumen / carbohydrate binding / secretory granule lumen / response to lipopolysaccharide / blood microparticle / G alpha (i) signalling events / immune response / receptor ligand activity / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / inflammatory response / signaling receptor binding / axon / innate immune response / serine-type endopeptidase activity / synapse / dendrite / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
: / : / Complement C4, MG1 domain / Complement C4A/B CUB C-terminal domain / Complement B/C2 / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment ...: / : / Complement C4, MG1 domain / Complement C4A/B CUB C-terminal domain / Complement B/C2 / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Anaphylatoxin, complement system domain / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Alpha-2-macroglobulin / Macroglobulin domain / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / von Willebrand factor type A domain / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Immunoglobulin-like fold / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Complement C3 / Complement C2 / Complement C4-B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYang XK / Xiao JY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Adv / Year: 2026
Title: Complement C3 Recognition by C3 Convertases
Authors: Yang XK / Xiao JY
History
DepositionMar 22, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63894.png

Downloads & links

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Map

FileDownload / File: emd_63894.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.95 Å
Density
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.61675483 - 1.0074946
Average (Standard dev.)0.00055603846 (±0.027630696)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 342.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63894_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63894_half_map_2.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 : CP/MBL pathways C3 convertases C4b2a and C3 complex

EntireName: CP/MBL pathways C3 convertases C4b2a and C3 complex
Components
  • Complex: CP/MBL pathways C3 convertases C4b2a and C3 complex
    • Protein or peptide: Serine protease complement C2b
    • Protein or peptide: Complement C3
    • Protein or peptide: Complement C4-B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: NICKEL (II) ION

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Supramolecule #1: CP/MBL pathways C3 convertases C4b2a and C3 complex

SupramoleculeName: CP/MBL pathways C3 convertases C4b2a and C3 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Serine protease complement C2b

MacromoleculeName: Serine protease complement C2b / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: classical-complement-pathway C3/C5 convertase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.491473 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KIQIQRSGHL NLYLLLDCSQ SVSENDFLIF KESASLMVDR IFSFEINVSV AIITFASEPK VLMSVLNDNS RDMTEVISSL ENANYKDHE NGTGTNTYAA LNSVYLMMNN QMRLLGMETM AWQEIRHAII LLTDGKSNMG GSPKTAVDHI REILNINQKR N DYLDIYAI ...String:
KIQIQRSGHL NLYLLLDCSQ SVSENDFLIF KESASLMVDR IFSFEINVSV AIITFASEPK VLMSVLNDNS RDMTEVISSL ENANYKDHE NGTGTNTYAA LNSVYLMMNN QMRLLGMETM AWQEIRHAII LLTDGKSNMG GSPKTAVDHI REILNINQKR N DYLDIYAI GVGKLDVDWR ELNELGSKKD GERHAFILQD TKALHQVFEH MLDVSKLTDT ICGVGNMSAN ASDQERTPWH VT IKPKSQE TCRGALISDQ WVLTAAHCFR DGNDHSLWRV NVGDPKSQWG KEFLIEKAVI SPGFDVFAKK NQGILEFYGD DIA LLKLAQ KVKMSTHARP ICLPCTMEAN LALRRPQGST CRDHENELLN KQSVPAHFVA LNGSKLNINL KMGVEWTSCA EVVS QEKTM FPNLTDVREV VTDQFLCSGT QEDESPCKGE SGGAVFLERR FRFFQVGLVS WGLYNPCLGS ADKNSRKRAP RSKVP PPRD FHINLFRMQP WLRQHLGDVL NFLPL

UniProtKB: Complement C2

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Macromolecule #2: Complement C3

MacromoleculeName: Complement C3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 187.370969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGPTSGPSLL LLLLTHLPLA LGSPMYSIIT PNILRLESEE TMVLEAHDAQ GDVPVTVTVH DFPGKKLVLS SEKTVLTPAT NHMGNVTFT IPANREFKSE KGRNKFVTVQ ATFGTQVVEK VVLVSLQSGY LFIQTDKTIY TPGSTVLYRI FTVNHKLLPV G RTVMVNIE ...String:
MGPTSGPSLL LLLLTHLPLA LGSPMYSIIT PNILRLESEE TMVLEAHDAQ GDVPVTVTVH DFPGKKLVLS SEKTVLTPAT NHMGNVTFT IPANREFKSE KGRNKFVTVQ ATFGTQVVEK VVLVSLQSGY LFIQTDKTIY TPGSTVLYRI FTVNHKLLPV G RTVMVNIE NPEGIPVKQD SLSSQNQLGV LPLSWDIPEL VNMGQWKIRA YYENSPQQVF STEFEVKEYV LPSFEVIVEP TE KFYYIYN EKGLEVTITA RFLYGKKVEG TAFVIFGIQD GEQRISLPES LKRIPIEDGS GEVVLSRKVL LDGVQNPRAE DLV GKSLYV SATVILHSGS DMVQAERSGI PIVTSPYQIH FTKTPKYFKP GMPFDLMVFV TNPDGSPAYR VPVAVQGEDT VQSL TQGDG VAKLSINTHP SQKPLSITVR TKKQELSEAE QATRTMQALP YSTVGNSNNY LHLSVLRTEL RPGETLNVNF LLRMD RAHE AKIRYYTYLI MNKGRLLKAG RQVREPGQDL VVLPLSITTD FIPSFRLVAY YTLIGASGQR EVVADSVWVD VKDSCV GSL VVKSGQSEDR QPVPGQQMTL KIEGDHGARV VLVAVDKGVF VLNKKNKLTQ SKIWDVVEKA DIGCTPGSGK DYAGVFS DA GLTFTSSSGQ QTAQRAELQC PQPAARRRRS VQLTEKRMDK VGKYPKELRK CCEDGMRENP MRFSCQRRTR FISLGEAC K KVFLDCCNYI TELRRQHARA SHLGLARSNL DEDIIAEENI VSRSEFPESW LWNVEDLKEP PKNGISTKLM NIFLKDSIT TWEILAVSMS DKKGICVADP FEVTVMQDFF IDLRLPYSVV RNEQVEIRAV LYNYRQNQEL KVRVELLHNP AFCSLATTKR RHQQTVTIP PKSSLSVPYV IVPLKTGLQE VEVKAAVYHH FISDGVRKSL KVVPEGIRMN KTVAVRTLDP ERLGREGVQK E DIPPADLS DQVPDTESET RILLQGTPVA QMTEDAVDAE RLKHLIVTPS GCGEQNMIGM TPTVIAVHYL DETEQWEKFG LE KRQGALE LIKKGYTQQL AFRQPSSAFA AFVKRAPSTW LTAYVVKVFS LAVNLIAIDS QVLCGAVKWL ILEKQKPDGV FQE DAPVIH QEMIGGLRNN NEKDMALTAF VLISLQEAKD ICEEQVNSLP GSITKAGDFL EANYMNLQRS YTVAIAGYAL AQMG RLKGP LLNKFLTTAK DKNRWEDPGK QLYNVEATSY ALLALLQLKD FDFVPPVVRW LNEQRYYGGG YGSTQATFMV FQALA QYQK DAPDHQELNL DVSLQLPSRS SKITHRIHWE SASLLRSEET KENEGFTVTA EGKGQGTLSV VTMYHAKAKD QLTCNK FDL KVTIKPAPET EKRPQDAKNT MILEICTRYR GDQDATMSIL DISMMTGFAP DTDDLKQLAN GVDRYISKYE LDKAFSD RN TLIIYLDKVS HSEDDCLAFK VHQYFNVELI QPGAVKVYAY YNLEESCTRF YHPEKEDGKL NKLCRDELCR CAEENCFI Q KSDDKVTLEE RLDKACEPGV DYVYKTRLVK VQLSNDFDEY IMAIEQTIKS GSDEVQVGQQ RTFISPIKCR EALKLEEKK HYLMWGLSSD FWGEKPNLSY IIGKDTWVEH WPEEDECQDE ENQKQCQDLG AFTESMVVFG CPN

UniProtKB: Complement C3

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Macromolecule #3: Complement C4-B

MacromoleculeName: Complement C4-B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 192.975188 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRLLWGLIWA SSFFTLSLQK PRLLLFSPSV VHLGVPLSVG VQLQDVPRGQ VVKGSVFLRN PSRNNVPCSP KVDFTLSSER DFALLSLQV PLKDAKSCGL HQLLRGPEVQ LVAHSPWLKD SLSRTTNIQG INLLFSSRRG HLFLQTDQPI YNPGQRVRYR V FALDQKMR ...String:
MRLLWGLIWA SSFFTLSLQK PRLLLFSPSV VHLGVPLSVG VQLQDVPRGQ VVKGSVFLRN PSRNNVPCSP KVDFTLSSER DFALLSLQV PLKDAKSCGL HQLLRGPEVQ LVAHSPWLKD SLSRTTNIQG INLLFSSRRG HLFLQTDQPI YNPGQRVRYR V FALDQKMR PSTDTITVMV ENSHGLRVRK KEVYMPSSIF QDDFVIPDIS EPGTWKISAR FSDGLESNSS TQFEVKKYVL PN FEVKITP GKPYILTVPG HLDEMQLDIQ ARYIYGKPVQ GVAYVRFGLL DEDGKKTFFR GLESQTKLVN GQSHISLSKA EFQ DALEKL NMGITDLQGL RLYVAAAIIE SPGGEMEEAE LTSWYFVSSP FSLDLSKTKR HLVPGAPFLL QALVREMSGS PASG IPVKV SATVSSPGSV PEVQDIQQNT DGSGQVSIPI IIPQTISELQ LSVSAGSPHP AIARLTVAAP PSGGPGFLSI ERPDS RPPR VGDTLNLNLR AVGSGATFSH YYYMILSRGQ IVFMNREPKR TLTSVSVFVD HHLAPSFYFV AFYYHGDHPV ANSLRV DVQ AGACEGKLEL SVDGAKQYRN GESVKLHLET DSLALVALGA LDTALYAAGS KSHKPLNMGK VFEAMNSYDL GCGPGGG DS ALQVFQAAGL AFSDGDQWTL SRKRLSCPKE KTTRKKRNVN FQKAINEKLG QYASPTAKRC CQDGVTRLPM MRSCEQRA A RVQQPDCREP FLSCCQFAES LRKKSRDKGQ AGLQRALEIL QEEDLIDEDD IPVRSFFPEN WLWRVETVDR FQILTLWLP DSLTTWEIHG LSLSKTKGLC VATPVQLRVF REFHLHLRLP MSVRRFEQLE LRPVLYNYLD KNLTVSVHVS PVEGLCLAGG GGLAQQVLV PAGSARPVAF SVVPTAATAV SLKVVARGSF EFPVGDAVSK VLQIEKEGAI HREELVYELN PLDHRGRTLE I PGNSDPNM IPDGDFNSYV RVTASDPLDT LGSEGALSPG GVASLLRLPR GCGEQTMIYL APTLAASRYL DKTEQWSTLP PE TKDHAVD LIQKGYMRIQ QFRKADGSYA AWLSRGSSTW LTAFVLKVLS LAQEQVGGSP EKLQETSNWL LSQQQADGSF QDL SPVIHR SMQGGLVGND ETVALTAFVT IALHHGLAVF QDEGAEPLKQ RVEASISKAS SFLGEKASAG LLGAHAAAIT AYAL TLTKA PADLRGVAHN NLMAMAQETG DNLYWGSVTG SQSNAVSPTP APRNPSDPMP QAPALWIETT AYALLHLLLH EGKAE MADQ AAAWLTRQGS FQGGFRSTQD TVIALDALSA YWIASHTTEE RGLNVTLSST GRNGFKSHAL QLNNRQIRGL EEELQF SLG SKINVKVGGN SKGTLKVLRT YNVLDMKNTT CQDLQIEVTV KGHVEYTMEA NEDYEDYEYD ELPAKDDPDA PLQPVTP LQ LFEGRRNRRR REAPKVVEEQ ESRVHYTVCI WRNGKVGLSG MAIADVTLLS GFHALRADLE KLTSLSDRYV SHFETEGP H VLLYFDSVPT SRECVGFEAV QEVPVGLVQP ASATLYDYYN PERRCSVFYG APSKSRLLAT LCSAEVCQCA EGKCPRQRR ALERGLQDED GYRMKFACYY PRVEYGFQVK VLREDSRAAF RLFETKITQV LHFTKDVKAA ANQMRNFLVR ASCRLRLEPG KEYLIMGLD GATYDLEGHP QYLLDSNSWI EEMPSERLCR STRQRAACAQ LNDFLQEYGT QGCQV

UniProtKB: Complement C4-B

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / 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 #7: NICKEL (II) ION

MacromoleculeName: NICKEL (II) ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: NI
Molecular weightTheoretical: 58.693 Da
Chemical component information

ChemComp-NI:
NICKEL (II) ION

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 109455
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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