9QPY | pdb_00009qpy

Structure of the Complement classical and lectin pathway C3 convertase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into C3 convertase activity of the classical pathway of complement.

De la O Becerra, K.I.Brondijk, T.H.C.Serna Martin, I.Gros, P.

(2025) Nat Commun 17: 993-993

  • DOI: https://doi.org/10.1038/s41467-025-67730-4
  • Primary Citation Related Structures: 
    9QJ4, 9QJ5, 9QK2, 9QPY

  • PubMed Abstract: 

    Immune protection by the complement system depends on C3 cleavage by C3 convertases that is critical to all three activation pathways. Structural data on convertase formation in the classical pathway and on C3-substrate binding to convertases is lacking. We present the cryo-EM structures of the proconvertase (C4b2), convertase (C4b2b), and convertase-substrate complex (C4b2b-C3) of the classical pathway. The data show that C2 and C4b form proconvertases and convertases like factor B and C3b of the alternative pathway. Substrate C3 binds C4b of the convertase through two interfaces: one also found in the SCIN-inhibited C3bBb dimer, and another facilitated by conformational changes in C3. Bending of C3 and swinging of the C2 protease bring the C3-scissile loop into the active site. The second, charged, C4b-interaction site favors C3- substrate binding, but upon cleavage repels product C3b. Thus, a charge switch-over mechanism effects the catalytic turnover of the convertases producing opsonin C3b.


  • Organizational Affiliation
    • Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Dept. of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C4-A
A, B, C
1,744Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0L4 (Homo sapiens)
Explore P0C0L4 
Go to UniProtKB:  P0C0L4
PHAROS:  P0C0L4
GTEx:  ENSG00000244731 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0L4
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P0C0L4-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Anti-C4b nanobody B12120Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C2752Homo sapiensMutation(s): 1 
Gene Names: C2
EC: 3.4.21.43
UniProt & NIH Common Fund Data Resources
Find proteins for P06681 (Homo sapiens)
Explore P06681 
Go to UniProtKB:  P06681
PHAROS:  P06681
GTEx:  ENSG00000166278 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06681
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P06681-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A]
G [auth B]
H [auth B]
I [auth B]
K [auth E]
F [auth A],
G [auth B],
H [auth B],
I [auth B],
K [auth E],
L [auth E],
M [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
J [auth E]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv4.2.0/4
MODEL REFINEMENTPHENIX2.21.1
MODEL REFINEMENTCoot0.9.8.94

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Consejo Nacional de Ciencia y Tecnologia (CONACYT)MexicoCVU 604718
Netherlands Organisation for Scientific Research (NWO)Netherlands01.80.104.00
European Research Council (ERC)European Union787241

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release
  • Version 1.1: 2026-03-04
    Changes: Data collection, Database references