9CMI

Cryo-EM structure of human claudin-4 complex with Clostridium perfringens enterotoxin, sFab COP-1, and Nanobody

• PDB DOI: https://doi.org/10.2210/pdb9CMI/pdb
• EM Map EMD-45749: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Clostridium perfringens
• Expression System: Trichoplusia ni
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2024-07-15 Released: 2024-08-07 
• Deposition Author(s): Vecchio, A.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.83 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Cryo-EM Structures of Clostridium perfringens Enterotoxin Bound to its Human Receptor, Claudin-4

Vecchio, A.J., Kossiakoff, A.A., Erramilli, S.K., Rathnayake, S.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy, gel filtration

Macromolecule Content

• Total Structure Weight: 123.27 kDa 
• Atom Count: 7,877 
• Modelled Residue Count: 1,025 
• Deposited Residue Count: 1,130 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Claudin-4	A	211	Homo sapiens	Mutation(s): 0  Gene Names: CLDN4, CPER, CPETR1, WBSCR8 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O14493 (Homo sapiens) Explore O14493  Go to UniProtKB:  O14493
PHAROS:  O14493 GTEx:  ENSG00000189143

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat-labile enterotoxin B chain	B	299	Clostridium perfringens	Mutation(s): 0  Gene Names: cpe
UniProt
Find proteins for P01558 (Clostridium perfringens) Explore P01558  Go to UniProtKB:  P01558

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
COP-1 sFab Heavy Chain	C [auth H]	261	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-Fab Nanobody	D [auth K]	121	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
COP-1 sFab Light Chain	E [auth L]	238	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AV0	F [auth H]	Lauryl Maltose Neopentyl Glycol C47 H88 O22 MADJBYLAYPCCOO-VWHTXWAPSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.83 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.4
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Vecchio, A.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM138368
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM117372

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release