9QK2 | pdb_00009qk2

Structure of the Complement classical and lectin pathway C3 convertase in complex with substrate C3

PDB DOI: https://doi.org/10.2210/pdb9QK2/pdb
EM Map EMD-53217: EMDB EMDataResource

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

Deposited: 2025-03-19 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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 1,052.22 kDa
Atom Count: 29,917
Modeled Residue Count: 3,793
Deposited Residue Count: 9,430
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C4-A	A, B [auth C], D [auth B]	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0L4
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain D [auth B]	Go to GlyGen: P0C0L4-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C2	C [auth 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06681
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain C [auth E]	Go to GlyGen: P06681-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-C4b nanobody B12	E [auth D]	120	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C3	F, G	1,663	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens) Explore P01024 Go to UniProtKB: P01024
PHAROS: P01024 GTEx: ENSG00000125730
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01024
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain F Focus chain G	Go to GlyGen: P01024-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth E] SDF format, chain K [auth E] SDF format, chain L [auth E] SDF format, chain M [auth E] SDF format, chain N [auth B] SDF format, chain O [auth F] SDF format, chain P [auth G] MOL2 format, chain H [auth A] MOL2 format, chain J [auth E] MOL2 format, chain K [auth E] MOL2 format, chain L [auth E] MOL2 format, chain M [auth E] MOL2 format, chain N [auth B] MOL2 format, chain O [auth F] MOL2 format, chain P [auth G] mmCIF format, chain H [auth A] mmCIF format, chain J [auth E] mmCIF format, chain K [auth E] mmCIF format, chain L [auth E] mmCIF format, chain M [auth E] mmCIF format, chain N [auth B] mmCIF format, chain O [auth F] mmCIF format, chain P [auth G]	H [auth A] J [auth E] K [auth E] L [auth E] M [auth E] H [auth A], J [auth E], K [auth E], L [auth E], M [auth E], N [auth B], O [auth F], P [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Focus chain J [auth E] Focus chain K [auth E] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth B] Focus chain O [auth F] Focus chain P [auth G] Interactions & Density Focus chain H [auth A] Focus chain J [auth E] Focus chain K [auth E] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth B] Focus chain O [auth F] Focus chain P [auth G]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth E] MOL2 format, chain I [auth E] mmCIF format, chain I [auth E]	I [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth E] Interactions & Density Focus chain I [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 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

View Full Validation Report

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.

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