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- EMDB-63895: AP pathways C3 convertase C3bBbP and C3 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63895
TitleAP pathways C3 convertase C3bBbP and C3 complex
Map data
Sample
  • Complex: AP pathways C3 convertases C3bBb and C3 complex
    • Protein or peptide: Complement C3
    • Protein or peptide: Complement factor B Bb
    • Protein or peptide: Properdin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: NICKEL (II) ION
KeywordsAP pathways / C3 convertases and substrate / C3bBbP_C3 complex / IMMUNE SYSTEM
Function / homology
Function and homology information


cytoplasmic side of Golgi membrane / alternative-complement-pathway C3/C5 convertase / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / complement binding / positive regulation of activation of membrane attack complex ...cytoplasmic side of Golgi membrane / alternative-complement-pathway C3/C5 convertase / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / complement binding / positive regulation of activation of membrane attack complex / 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 / 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 / Peptide ligand-binding receptors / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / fatty acid metabolic process / positive regulation of immune response / positive regulation of receptor-mediated endocytosis / specific granule lumen / 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 / tertiary granule lumen / secretory granule lumen / blood microparticle / G alpha (i) signalling events / defense response to bacterium / immune response / receptor ligand activity / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / inflammatory response / signaling receptor binding / serine-type endopeptidase activity / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / : / Thrombospondin type 1 repeat / CFP-like, C-terminal thrombospondin type 1 domain / : / Complement factor B / Complement B/C2 / Complement C3-like, NTR domain / : / : ...: / : / Thrombospondin type 1 repeat / CFP-like, C-terminal thrombospondin type 1 domain / : / Complement factor B / 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 / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / 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
Similarity search - Domain/homology
Complement factor B / Complement C3 / Properdin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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_63895.png

Downloads & links

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Map

FileDownload / File: emd_63895.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-1.1682196 - 1.78516
Average (Standard dev.)-0.000029801187 (±0.04623179)
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_63895_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_63895_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 : AP pathways C3 convertases C3bBb and C3 complex

EntireName: AP pathways C3 convertases C3bBb and C3 complex
Components
  • Complex: AP pathways C3 convertases C3bBb and C3 complex
    • Protein or peptide: Complement C3
    • Protein or peptide: Complement factor B Bb
    • Protein or peptide: Properdin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: NICKEL (II) ION

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Supramolecule #1: AP pathways C3 convertases C3bBb and C3 complex

SupramoleculeName: AP pathways C3 convertases C3bBb 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: Complement C3

MacromoleculeName: Complement C3 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / 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 #2: Complement factor B Bb

MacromoleculeName: Complement factor B Bb / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.116121 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KIVLDPSGSM NIYLVLDGSD SIGASNFTGA KKCLVNLIEK VASYGVKPRY GLVTYATYPK IWVKVSEADS SNADWVTKQL NEINYEDHK LKSGTNTKKA LQAVYSMMSW PDDVPPEGWN RTRHVIILMT DGLHNMGGDP ITVIDEIRDL LYIGKDRKNP R EDYLDVYV ...String:
KIVLDPSGSM NIYLVLDGSD SIGASNFTGA KKCLVNLIEK VASYGVKPRY GLVTYATYPK IWVKVSEADS SNADWVTKQL NEINYEDHK LKSGTNTKKA LQAVYSMMSW PDDVPPEGWN RTRHVIILMT DGLHNMGGDP ITVIDEIRDL LYIGKDRKNP R EDYLDVYV FGVGPLVNQV NINALASKKD NEQHVFKVKD MENLEDVFYQ MIDESQSLSL CGMVWEHRKG TDYHKQPWQA KI SVIRPSK GHESCMGAVV SEYFVLTAAH CFTVDDKEHS IKVSVGGEKR DLEIEVVLFH PNYNINGKKE AGIPEFYDYD VAL IKLKNK LKYGQTIRPI CLPCTEGTTR ALRLPPTTTC QQQKEELLPA QDIKALFVSE EEKKLTRKEV YIKNGDKKGS CERD AQYAP GYDKVKDISE VVTPRFLCTG GVSPYADPNT CRGDSGGPLI VHKRSRFIQV GVISWGVVDV CKNQKRQKQV PAHAR DFHI NLFQVLPWLK EKLQDEDLGF L

UniProtKB: Complement factor B

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Macromolecule #3: Properdin

MacromoleculeName: Properdin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.544359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MITEGAQAPR LLLPPLLLLL TLPATGSDPV LCFTQYEESS GKCKGLLGGG VSVEDCCLNT AFAYQKRSGG LCQPCRSPRW SLWSTWAPC SVTCSEGSQL RYRRCVGWNG QCSGKVAPGT LEWQLQACED QQCCPEMGGW SGWGPWEPCS VTCSKGTRTR R RACNHPAP ...String:
MITEGAQAPR LLLPPLLLLL TLPATGSDPV LCFTQYEESS GKCKGLLGGG VSVEDCCLNT AFAYQKRSGG LCQPCRSPRW SLWSTWAPC SVTCSEGSQL RYRRCVGWNG QCSGKVAPGT LEWQLQACED QQCCPEMGGW SGWGPWEPCS VTCSKGTRTR R RACNHPAP KCGGHCPGQA QESEACDTQQ VCPTHGAWAT WGPWTPCSAS CHGGPHEPKE TRSRKCSAPE PSQKPPGKPC PG LAYEQRR CTGLPPCPVA GGWGPWGPVS PCPVTCGLGQ TMEQRTCNHP VPQHGGPFCA GDATRTHICN TAVPCPVDGE WDS WGEWSP CIRRNMKSIS CQEIPGQQSR GRTCRGRKFD GHRCAGQQQD IRHCYSIQHC PLKGSWSEWS TWGLCMPPCG PNPT RARQR LCTPLLPKYP PTVSMVEGQG EKNVTFWGRP LPRCEELQGQ KLVVEEKR

UniProtKB: Properdin

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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: 5 / 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: NICKEL (II) ION

MacromoleculeName: NICKEL (II) ION / type: ligand / ID: 6 / 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: 8
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: cryos / Type: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 389342
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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