9VCA | pdb_00009vca

Binding site between C-reactive protein and c2cc monoclonal antibody

• PDB DOI: https://doi.org/10.2210/pdb9VCA/pdb
• EM Map EMD-64950: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Mus musculus albula
• Expression System: Homo sapiens, Mus musculus albula
• Mutation(s): No 


• Deposited: 2025-06-05 Released: 2025-11-19 
• Deposition Author(s): Moiseenko, A.V., Kalikin, A.V.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Cryo-EM structure of pentameric C-reactive protein in complex with monoclonal IgG antibodies.

Moiseenko, A.V., Kalikin, A.V., Orekhov, P.S., Byzova, N.A., Zherdev, A.V., Shaitan, K.V., Dzantiev, B.B., Sokolova, O.S.

(2025) FEBS J 

• PubMed: 41159871 
• DOI: https://doi.org/10.1111/febs.70310
• Primary Citation of Related Structures:  
  9VCA


• PubMed Abstract: 
  

  C-reactive protein (CRP) plays a central role in innate immunity and serves as a key biomarker of inflammation. Despite its clinical importance, the structural basis of CRP interactions with antibodies remains poorly characterized. Using cryo-electron microscopy (cryo-EM), we resolved the structure of immune complexes formed between pentameric CRP and monoclonal immunoglobulin G (IgG) antibodies at up to 2.4 Å resolution. The complexes display a barrel-shaped architecture, with two CRP pentamers bridged by three to five antibodies. We built an atomic model of the CRP-antibody interface, identifying a binding site on the A-face of CRP mediated exclusively by hydrogen bonds, without salt-bridge formation. These findings provide structural insights into CRP-IgG recognition and offer a basis for the rational design of improved antibodies.

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Organizational Affiliation: 
• Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.
Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, China.
A.N. Bach Institute of Biochemistry, The Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow, Russia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 96.1 kDa 
• Atom Count: 3,394 
• Modeled Residue Count: 433 
• Deposited Residue Count: 867 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-reactive protein	A [auth E]	206	Homo sapiens	Mutation(s): 0  Gene Names: CRP, PTX1
UniProt & NIH Common Fund Data Resources
Find proteins for P02741 (Homo sapiens) Explore P02741  Go to UniProtKB:  P02741
PHAROS:  P02741 GTEx:  ENSG00000132693

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Monoclonal IgG antibody heavy chain fragment	B [auth H]	443	Mus musculus albula	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Monoclonal IgG antibody light chain fragment	C [auth L]	218	Mus musculus albula	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	ISOLDE	1.8
MODEL REFINEMENT	PHENIX	1.20
RECONSTRUCTION	cryoSPARC	4.6

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Moiseenko, A.V., Kalikin, A.V.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release