9CMI | pdb_00009cmi

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

External Resource: Annotation

Domain Annotation: SCOP2 Classification
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: PDBTM

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Claudin-like	8092547	3002606	SCOP2B (2022-06-29)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
C [auth H]	Fab COP-1	1C-1C-LIKE-CH2-CH3	Homo sapiens (human)	IGHV3-2304, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG105, IGHG112, IGHG114, IGHG113, IGHG109, IGHG110, IGHG107, IGHG111, IGHG115, IGHG1*16	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202548-0)
D [auth K]	nAb	VH	Homo sapiens (human)	IGHV3-2301, IGHV3-23D01, IGHJ401, IGHJ402, IGHJ4*03	V-DOMAIN VH	IG	VH	IMGT (202548-0)
E [auth L]	Fab COP-1	L-KAPPA	Homo sapiens (human)	IGKV1-3901, IGKV1D-3901, IGKJ101, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202548-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth H]	Heavy Chain	IGHV3	-	claudin-4 \| heat-labile enterotoxin b chain	SAbDab (2025-12-12)
D [auth K]	Heavy Chain	IGHV1	-	-	SAbDab (2025-12-12)
E [auth L]	Light Chain	IGKV1	Kappa	claudin-4 \| heat-labile enterotoxin b chain	SAbDab (2025-12-12)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF03505	Clostridium enterotoxin (Clenterotox)	Clostridium enterotoxin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Claudin-4	monoatomic anion transmembrane transporter activity chloride transmembrane transporter activity passive transmembrane transporter activity monoatomic ion channel activity channel activity monoatomic anion channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity chloride channel activity structural molecule activity identical protein binding protein binding binding monoatomic anion transmembrane transporter activity chloride transmembrane transporter activity passive transmembrane transporter activity monoatomic ion channel activity channel activity monoatomic anion channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity chloride channel activity structural molecule activity identical protein binding protein binding binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity	rhythmic process circadian rhythm calcium-independent cell-cell adhesion cell adhesion cell-cell adhesion cellular process positive regulation of response to wounding wound healing regulation of biological process response to stimulus biological regulation positive regulation of biological process regulation of response to wounding positive regulation of response to stimulus rhythmic process circadian rhythm calcium-independent cell-cell adhesion cell adhesion cell-cell adhesion cellular process positive regulation of response to wounding wound healing regulation of biological process response to stimulus biological regulation positive regulation of biological process regulation of response to wounding positive regulation of response to stimulus positive regulation of wound healing regulation of response to stimulus response to stress regulation of response to stress regulation of wound healing response to wounding multi-multicellular organism process multicellular organismal process reproductive process female pregnancy multi-organism reproductive process response to ketone response to lipid response to hormone response to steroid hormone response to chemical response to endogenous stimulus response to progesterone response to oxygen-containing compound developmental process establishment of skin barrier epithelium development skin development skin epidermis development epidermis development anatomical structure development animal organ development tissue development anatomical structure morphogenesis regulation of developmental process cell morphogenesis regulation of cell morphogenesis regulation of anatomical structure morphogenesis bicellular tight junction assembly tight junction organization apical junction assembly cellular component organization cellular component biogenesis cell junction organization cellular component assembly cell junction assembly tight junction assembly cellular component organization or biogenesis cell-cell junction assembly cell-cell junction organization renal system process system process renal absorption positive regulation of locomotion regulation of cell motility regulation of cellular process positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion positive regulation of cellular process localization transport paracellular transport establishment of localization	protein-containing complex cellular anatomical structure transmembrane transporter complex membrane chloride channel complex membrane protein complex transporter complex monoatomic ion channel complex cell-cell junction anchoring junction cell junction cell periphery apical part of cell plasma membrane protein-containing complex cellular anatomical structure transmembrane transporter complex membrane chloride channel complex membrane protein complex transporter complex monoatomic ion channel complex cell-cell junction anchoring junction cell junction cell periphery apical part of cell plasma membrane plasma membrane region apical plasma membrane basal part of cell basal plasma membrane apicolateral plasma membrane apical junction complex bicellular tight junction tight junction lateral plasma membrane
B	Heat-labile enterotoxin B chain	toxin activity	-	cellular anatomical structure extracellular region
C [auth H]	COP-1 sFab Heavy Chain	-	-	-
D [auth K]	Anti-Fab Nanobody	-	-	-
E [auth L]	COP-1 sFab Light Chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006187	Claudin	Family
A	IPR004031	PMP-22/EMP/MP20/Claudin	Family
A	IPR017974	Claudin, conserved site	Conserved Site
A	IPR003550	Claudin-4	Family
B	IPR003897	Clostridium enterotoxin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O14493	polycystic ovary syndrome invasive ductal breast carcinoma breast carcinoma Neoplasm Recurrence, Local breast cancer gastric carcinoma lung adenocarcinoma malignant pancreatic neoplasm ovarian cancer Williams syndrome interstitial cystitis malignant mesothelioma pancreatic intraductal papillary-mucinous carcinoma ductal breast carcinoma in situ osteosarcoma polycystic ovary syndrome invasive ductal breast carcinoma breast carcinoma Neoplasm Recurrence, Local breast cancer gastric carcinoma lung adenocarcinoma malignant pancreatic neoplasm ovarian cancer Williams syndrome interstitial cystitis malignant mesothelioma pancreatic intraductal papillary-mucinous carcinoma ductal breast carcinoma in situ osteosarcoma pancreatic intraductal papillary-mucinous neoplasm

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A	PDBTM	Annotated as membrane protein by PDBTM

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.