9QPY | pdb_00009qpy

Structure of the Complement classical and lectin pathway C3 convertase

• PDB DOI: https://doi.org/10.2210/pdb9QPY/pdb
• EM Map EMD-53288: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Lama glama
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): Yes 


• Deposited: 2025-03-31 Released: 2025-12-24 
• Deposition Author(s): De la O Becerra, K.I., Brondijk, T.H.C., Gros, P.
• Funding Organization(s): Consejo Nacional de Ciencia y Tecnologia (CONACYT), Netherlands Organisation for Scientific Research (NWO), European Research Council (ERC)

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Experimental Data Snapshot

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

Starting Models: experimental

Literature

Mechanistic insights into complement classical pathway C3 convertase based on cryo-EM structures

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 677.22 kDa 
• Atom Count: 16,917 
• Modeled Residue Count: 2,154 
• Deposited Residue Count: 6,104 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C4-A	A, B, C	1,744	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0L4 (Homo sapiens) Explore P0C0L4  Go to UniProtKB:  P0C0L4
PHAROS:  P0C0L4 GTEx:  ENSG00000244731
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P0C0L4-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-C4b nanobody B12	D	120	Lama glama	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C2	E	752	Homo sapiens	Mutation(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
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P06681-1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	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	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:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v4.2.0/4
MODEL REFINEMENT	PHENIX	2.21.1
MODEL REFINEMENT	Coot	0.9.8.94

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): De la O Becerra, K.I., Brondijk, T.H.C., Gros, P.

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Funding Organization	Location	Grant Number
Consejo Nacional de Ciencia y Tecnologia (CONACYT)	Mexico	CVU 604718
Netherlands Organisation for Scientific Research (NWO)	Netherlands	01.80.104.00
European Research Council (ERC)	European Union	787241

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release