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- EMDB-53288: Structure of the Complement classical and lectin pathway C3 convertase -

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Basic information

Entry
Database: EMDB / ID: EMD-53288
TitleStructure of the Complement classical and lectin pathway C3 convertase
Map dataSharpened map of Complement C4b in complex with C2b and anti-C4b nanobody NbB12
Sample
  • Complex: Classical and lectin pathway C3 convertase
    • Protein or peptide: Complement C4-A
    • Protein or peptide: Anti-C4b nanobody B12
    • Protein or peptide: Complement C2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: MAGNESIUM ION
KeywordsC3 convertase / Complement classical pathway / convertase complex / Enzyme / IMMUNE SYSTEM
Function / homology
Function and homology information


classical-complement-pathway C3/C5 convertase / complement component C1q complex 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 ...classical-complement-pathway C3/C5 convertase / complement component C1q complex 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 / Post-translational protein phosphorylation / response to bacterium / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood microparticle / response to lipopolysaccharide / endoplasmic reticulum lumen / inflammatory response / axon / innate immune response / serine-type endopeptidase activity / neuronal cell body / 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-A
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsDe la O Becerra KI / Brondijk THC / Gros P
Funding support Mexico, Netherlands, European Union, 3 items
OrganizationGrant numberCountry
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)787241European Union
CitationJournal: To Be Published
Title: Mechanistic insights into complement classical pathway C3 convertase based on cryo-EM structures
Authors: De la O Becerra KI / Brondijk THC / Serna Martin I / Gros P
History
DepositionMar 31, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53288.png

Downloads & links

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Map

FileDownload / File: emd_53288.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of Complement C4b in complex with C2b and anti-C4b nanobody NbB12
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 380 pix.
= 395.2 Å		1.04 Å/pix.
x 380 pix.
= 395.2 Å		1.04 Å/pix.
x 380 pix.
= 395.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.41580757 - 0.8354834
Average (Standard dev.)-0.0003474877 (±0.019363714)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 395.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53288_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_53288_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map of Complement C4b in complex with...

Fileemd_53288_additional_1.map
AnnotationUnsharpened map of Complement C4b in complex with C2b and anti-C4b nanobody NbB12
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local resolution map of Complement C4b in complex...

Fileemd_53288_additional_2.map
AnnotationLocal resolution map of Complement C4b in complex with C2b and C4b nanobody NbB12
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of Complement C4b in complex...

Fileemd_53288_half_map_1.map
AnnotationHalf map A of Complement C4b in complex with C2b and C4b nanobody NbB12
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of Complement C4b in complex...

Fileemd_53288_half_map_2.map
AnnotationHalf map B of Complement C4b in complex with C2b and C4b nanobody NbB12
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Classical and lectin pathway C3 convertase

EntireName: Classical and lectin pathway C3 convertase
Components
  • Complex: Classical and lectin pathway C3 convertase
    • Protein or peptide: Complement C4-A
    • Protein or peptide: Anti-C4b nanobody B12
    • Protein or peptide: Complement C2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Classical and lectin pathway C3 convertase

SupramoleculeName: Classical and lectin pathway C3 convertase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 268 KDa

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Macromolecule #1: Complement C4-A

MacromoleculeName: Complement C4-A / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: blood plasma
Molecular weightTheoretical: 192.993203 KDa
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 SVVPTAAAAV SLKVVARGSF EFPVGDAVSK VLQIEKEGAI HREELVYELN PLDHRGRTLE I PGNSDPNM IPDGDFNSYV RVTASDPLDT LGSEGALSPG GVASLLRLPR GCGEQTMIYL APTLAASRYL DKTEQWSTLP PE TKDHAVD LIQKGYMRIQ QFRKADGSYA AWLSRDSSTW LTAFVLKVLS LAQEQVGGSP EKLQETSNWL LSQQQADGSF QDP CPVLDR SMQGGLVGND ETVALTAFVT IALHHGLAVF QDEGAEPLKQ RVEASISKAN SFLGEKASAG LLGAHAAAIT AYAL SLTKA PVDLLGVAHN NLMAMAQETG DNLYWGSVTG SQSNAVSPTP APRNPSDPMP QAPALWIETT AYALLHLLLH EGKAE MADQ ASAWLTRQGS 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-A

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Macromolecule #2: Anti-C4b nanobody B12

MacromoleculeName: Anti-C4b nanobody B12 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.322883 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EVQLVESGGG LVQAGGSLRL SCVASERTYM AWFRQAPGKE REFVAAITSS GMMTEYAPSV KGRFTISRDN AKNTVYLQMN SLKPEDTAV YYCAADLRQR FGERVTEYDY WGQGTQVTVS S

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Macromolecule #3: Complement C2

MacromoleculeName: Complement C2 / type: protein_or_peptide / ID: 3 / Details: Active site mutation S679A / Number of copies: 1 / Enantiomer: LEVO / EC number: classical-complement-pathway C3/C5 convertase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.347766 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 SPCKGEAGGA VFLERRFRFF QVGLVSWGLY NPCLGSADKN SRKRAPRS K VPPPRDFHIN LFRMQPWLRQ HLGDVLNFLP L

UniProtKB: Complement C2

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 7 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration0.23 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloride
20.0 mMHEPES
2.0 mMMgCl2Magnesium chloride
2.0 mMCaCl2Clacium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 20 mAmp
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsComplex of C3 conversase with anti-C4b nanobody b12

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4276 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v4.2.0/4) / Type: NONE
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.2.0/4) / Number images used: 17283
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.2.0/4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.2.0/4)
Final 3D classificationSoftware - Name: cryoSPARC (ver. v4.2.0/4)

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Atomic model buiding 1

Initial model
PDB IDChain

5jtw

chain_id: A, source_name: PDB, initial_model_type: experimental model

5jtw

chain_id: B, source_name: PDB, initial_model_type: experimental model

5jtw

chain_id: C, source_name: PDB, initial_model_type: experimental model

7b2q

chain_id: D, source_name: PDB, initial_model_type: experimental model

2i6q

chain_id: E, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9qpy:
Structure of the Complement classical and lectin pathway C3 convertase

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