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- PDB-9qk2: Structure of the Complement classical and lectin pathway C3 conve... -

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Basic information

Entry
Database: PDB / ID: 9qk2
TitleStructure of the Complement classical and lectin pathway C3 convertase in complex with substrate C3
Components
  • Anti-C4b nanobody B12
  • Complement C2
  • Complement C3
  • Complement C4-A
KeywordsIMMUNE SYSTEM / C3 convertase / Complement classical pathway / convertase-substrate complex / C3 substrate
Function / homology
Function and homology information


classical-complement-pathway C3/C5 convertase / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement component C1q complex binding / response to thyroid hormone / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning ...classical-complement-pathway C3/C5 convertase / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement component C1q complex binding / 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 / positive regulation of protein phosphorylation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / secretory granule lumen / blood microparticle / G alpha (i) signalling events / response to lipopolysaccharide / 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 / neuronal cell body / 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 / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / 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-A
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDe la O Becerra, K.I. / Brondijk, T.H.C. / Gros, P.
Funding support Mexico, Netherlands, European Union, 3items
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, K.I. / Brondijk, T.H.C. / Serna Martin, I. / Gros, P.
History
DepositionMar 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.0Dec 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C4-A
C: Complement C4-A
E: Complement C2
B: Complement C4-A
D: Anti-C4b nanobody B12
F: Complement C3
G: Complement C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,052,21816
Polymers1,050,4247
Non-polymers1,7949
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 3 types, 6 molecules ACBEFG

#1: Protein Complement C4-A / Acidic complement C4 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 2


Mass: 192993.203 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: blood plasma / References: UniProt: P0C0L4
#2: Protein Complement C2 / C3/C5 convertase


Mass: 83347.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Active site mutation S679A / Source: (gene. exp.) Homo sapiens (human) / Gene: C2 / Details (production host): CMV promotor / Cell line (production host): HEK293 E+ / Production host: Homo sapiens (human)
References: UniProt: P06681, classical-complement-pathway C3/C5 convertase
#4: Protein Complement C3 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1


Mass: 187387.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: blood plasma / References: UniProt: P01024

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Antibody / Sugars / Non-polymers , 3 types, 10 molecules D

#3: Antibody Anti-C4b nanobody B12


Mass: 13322.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pET-X13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)pLysS
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Classical and lectin pathway C3 convertase in complex with substrate C3
Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Molecular weightValue: 0.452 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human) / Tissue: blood plasma
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
220 mMHEPES1
32 mMMagnesium chlorideMgCl21
42 mMClacium chlorideCaCl21
SpecimenConc.: 0.23 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: C4b and C3 were purified linked through 2 non-inhibitory nanobodies, for the classical and lectin pathways, targeting C4b-MG8 and C3-C345C domains. Then the complex was formed by addition of ...Details: C4b and C3 were purified linked through 2 non-inhibitory nanobodies, for the classical and lectin pathways, targeting C4b-MG8 and C3-C345C domains. Then the complex was formed by addition of C2 and preactivated C1s before freezing the grids.
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4276

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.2.0/4particle selection
2EPU2.10.0image acquisition
4cryoSPARCv4.2.0/4CTF correction
7UCSF ChimeraX1.7model fitting
9cryoSPARCv4.2.0/4initial Euler assignment
10cryoSPARCv4.2.0/4final Euler assignment
11cryoSPARCv4.2.0/4classification
12cryoSPARCv4.2.0/43D reconstruction
19PHENIX2.21.1model refinement
20Coot0.9.8.94model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 177801 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeChain-IDInitial refinement model-ID
15JTW

5jtw

A5JTWA1
25JTW

5jtw

B5JTWB1
35JTW

5jtw

C5JTWC1
42ODP

2odp

E2ODPE
57B2Q

7b2q

D7B2QD3
62A73

2a73

F2A73F4
72A73

2a73

G2A73G4
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00330523
ELECTRON MICROSCOPYf_angle_d0.55141360
ELECTRON MICROSCOPYf_dihedral_angle_d5.6374356
ELECTRON MICROSCOPYf_chiral_restr0.0434670
ELECTRON MICROSCOPYf_plane_restr0.0045355

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