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- EMDB-63893: C3 convertases zymogen C4b2 in loading state -

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Basic information

Entry
Database: EMDB / ID: EMD-63893
TitleC3 convertases zymogen C4b2 in loading state
Map data
Sample
  • Complex: complement system C4b2 zymogen in loading state
    • Protein or peptide: Complement C2
    • Protein or peptide: Complement C4-B
  • Ligand: NICKEL (II) ION
Keywordscomplement system / classical passway / C3 convertases zymogen / loading state / IMMUNOSUPPRESSANT
Function / homology
Function and homology information


classical-complement-pathway C3/C5 convertase / detection of molecule of bacterial origin / symbiont cell surface / opsonization / complement binding / response to thyroid hormone / positive regulation of apoptotic cell clearance / Activation of C3 and C5 / complement activation / endopeptidase inhibitor activity ...classical-complement-pathway C3/C5 convertase / detection of molecule of bacterial origin / symbiont cell surface / opsonization / complement binding / response to thyroid hormone / positive regulation of apoptotic cell clearance / Activation of C3 and C5 / complement activation / endopeptidase inhibitor activity / Initial triggering of complement / complement activation, classical pathway / response to nutrient / Regulation of Complement cascade / response to bacterium / carbohydrate binding / response to lipopolysaccharide / blood microparticle / inflammatory response / axon / innate immune response / serine-type endopeptidase activity / synapse / dendrite / 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 / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Anaphylatoxin, complement system domain / : / Alpha-macro-globulin thiol-ester bond-forming region ...: / : / Complement C4, MG1 domain / Complement C4A/B CUB C-terminal domain / Complement B/C2 / 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 C2 / Complement C4-B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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_63893.png

Downloads & links

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Map

FileDownload / File: emd_63893.map.gz / Format: CCP4 / Size: 103 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-0.73168045 - 1.269001
Average (Standard dev.)0.000461837 (±0.033454638)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 285.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63893_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_63893_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 : complement system C4b2 zymogen in loading state

EntireName: complement system C4b2 zymogen in loading state
Components
  • Complex: complement system C4b2 zymogen in loading state
    • Protein or peptide: Complement C2
    • Protein or peptide: Complement C4-B
  • Ligand: NICKEL (II) ION

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Supramolecule #1: complement system C4b2 zymogen in loading state

SupramoleculeName: complement system C4b2 zymogen in loading state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Complement C2

MacromoleculeName: Complement C2 / 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: 83.363766 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGPLMVLFCL LFLYPGLADS APSCPQNVNI SGGTFTLSHG WAPGSLLTYS CPQGLYPSPA SRLCKSSGQW QTPGATRSLS KAVCKPVRC PAPVSFENGI YTPRLGSYPV GGNVSFECED GFILRGSPVR QCRPNGMWDG ETAVCDNGAG HCPNPGISLG A VRTGFRFG ...String:
MGPLMVLFCL LFLYPGLADS APSCPQNVNI SGGTFTLSHG WAPGSLLTYS CPQGLYPSPA SRLCKSSGQW QTPGATRSLS KAVCKPVRC PAPVSFENGI YTPRLGSYPV GGNVSFECED GFILRGSPVR QCRPNGMWDG ETAVCDNGAG HCPNPGISLG A VRTGFRFG HGDKVRYRCS SNLVLTGSSE RECQGNGVWS GTEPICRQPY SYDFPEDVAP ALGTSFSHML GATNPTQKTK ES LGRKIQI QRSGHLNLYL LLDCSQSVSE NDFLIFKESA SLMVDRIFSF EINVSVAIIT FASEPKVLMS VLNDNSRDMT EVI SSLENA NYKDHENGTG TNTYAALNSV YLMMNNQMRL LGMETMAWQE IRHAIILLTD GKSNMGGSPK TAVDHIREIL NINQ KRNDY LDIYAIGVGK LDVDWRELNE LGSKKDGERH AFILQDTKAL HQVFEHMLDV SKLTDTICGV GNMSANASDQ ERTPW HVTI KPKSQETCRG ALISDQWVLT AAHCFRDGND HSLWRVNVGD PKSQWGKEFL IEKAVISPGF DVFAKKNQGI LEFYGD DIA LLKLAQKVKM STHARPICLP CTMEANLALR RPQGSTCRDH ENELLNKQSV PAHFVALNGS KLNINLKMGV EWTSCAE VV SQEKTMFPNL TDVREVVTDQ FLCSGTQEDE SPCKGESGGA VFLERRFRFF QVGLVSWGLY NPCLGSADKN SRKRAPRS K VPPPRDFHIN LFRMQPWLRQ HLGDVLNFLP L

UniProtKB: Complement C2

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Macromolecule #2: Complement C4-B

MacromoleculeName: Complement C4-B / type: protein_or_peptide / ID: 2 / 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 #3: NICKEL (II) ION

MacromoleculeName: NICKEL (II) ION / type: ligand / ID: 3 / 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 correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 109606
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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