9V32 | pdb_00009v32

Human claudin 18.2 in complex with the Fab fragment of Zolbetuximab

• PDB DOI: https://doi.org/10.2210/pdb9V32/pdb
• EM Map EMD-64747: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Komagataella pastoris, Escherichia coli
• Mutation(s): No 


• Deposited: 2025-05-21 Released: 2026-05-27 
• Deposition Author(s): Wang, X., Ma, H., Fu, C., Sun, Z., Su, Z., Zhou, X.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Recognition of human claudin 18.2 by therapeutic antibodies

Wang, X., Fu, C., Ma, H., Yang, P., Sun, Z., Su, Z., Zhou, X.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 73.73 kDa 
• Atom Count: 4,507 
• Modeled Residue Count: 593 
• Deposited Residue Count: 680 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform A2 of Claudin-18	A	211	Homo sapiens	Mutation(s): 0  Gene Names: CLDN18, UNQ778/PRO1572
UniProt & NIH Common Fund Data Resources
Find proteins for P56856 (Homo sapiens) Go to UniProtKB:  P56856
PHAROS:  P56856 GTEx:  ENSG00000066405

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab of Zolbetuximab - Heavy chain	B [auth H]	249	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab of Zolbetuximab - Light chain	C [auth L]	220	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.4
MODEL REFINEMENT	PHENIX	1.19.1_4122:

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-27 
Deposition Author(s): Wang, X., Ma, H., Fu, C., Sun, Z., Su, Z., Zhou, X.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-05-27
  Type: Initial release