4QD2 | pdb_00004qd2

Molecular basis for disruption of E-cadherin adhesion by botulinum neurotoxin A complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
J	d4qd2j1	All beta proteins	Immunoglobulin-like beta-sandwich	Cadherin-like	Cadherin	E-cadherin (epithelial)	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d4qd2e1	All beta proteins	Immunoglobulin-like beta-sandwich	Cadherin-like	Cadherin	E-cadherin (epithelial)	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
H	d4qd2h1	All beta proteins	beta-Trefoil	Ricin B-like lectins	automated matches	automated matches	(Clostridium botulinum A str. Hall ) [TaxId: 441771 ],	SCOPe (2.08)
H	d4qd2h3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Clostridium botulinum A str. Hall ) [TaxId: 441771 ],	SCOPe (2.08)
F [auth I]	d4qd2i1	All beta proteins	beta-Trefoil	Ricin B-like lectins	automated matches	automated matches	(Clostridium botulinum A str. Hall ) [TaxId: 441771 ],	SCOPe (2.08)
F [auth I]	d4qd2i3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Clostridium botulinum A str. Hall ) [TaxId: 441771 ],	SCOPe (2.08)
C	d4qd2c1	All beta proteins	beta-Trefoil	Ricin B-like lectins	automated matches	automated matches	(Clostridium botulinum A str. Hall ) [TaxId: 441771 ],	SCOPe (2.08)
C	d4qd2c2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Clostridium botulinum A str. Hall ) [TaxId: 441771 ],	SCOPe (2.08)
A [auth D]	d4qd2d2	All beta proteins	beta-Trefoil	Ricin B-like lectins	automated matches	automated matches	(Clostridium botulinum A str. Hall ) [TaxId: 441771 ],	SCOPe (2.08)
A [auth D]	d4qd2d3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Clostridium botulinum A str. Hall ) [TaxId: 441771 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J	SCOP2B Superfamily	Cadherin-like	8055233	3002049	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Cadherin-like	8055233	3002049	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
J	Cadherin	e4qd2J2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Cadherin	ECOD (1.6)
E	Cadherin	e4qd2E2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Cadherin	ECOD (1.6)
I [auth F]	EUF07615	e4qd2F1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: EUF07615	ECOD (1.6)
I [auth F]	Clenterotox_C	e4qd2F2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: Clenterotox_C	ECOD (1.6)
D [auth A]	EUF07615	e4qd2A1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: EUF07615	ECOD (1.6)
D [auth A]	Clenterotox_C	e4qd2A2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: Clenterotox_C	ECOD (1.6)
G	Botulinum_HA-17	e4qd2G1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: Botulinum_HA-17	ECOD (1.6)
B	Botulinum_HA-17	e4qd2B1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: Botulinum_HA-17	ECOD (1.6)
H	RicinB_lectin_2	e4qd2H1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: RicinB_lectin_2	ECOD (1.6)
F [auth I]	RicinB_lectin_2	e4qd2I1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: RicinB_lectin_2	ECOD (1.6)
C	RicinB_lectin_2	e4qd2C1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: RicinB_lectin_2	ECOD (1.6)
A [auth D]	RicinB_lectin_2	e4qd2D1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: RicinB_lectin_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J	2.60.40.60	Mainly Beta	Sandwich	Immunoglobulin-like	Cadherins	CATH (4.3.0)
E	2.60.40.60	Mainly Beta	Sandwich	Immunoglobulin-like	Cadherins	CATH (4.3.0)
I [auth F]	2.60.120.1090	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
D [auth A]	2.60.120.1090	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
G	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
B	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
H	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
F [auth I]	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
C	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
A [auth D]	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, J	PF00028	Cadherin domain (Cadherin)	Cadherin domain		Domain
D [auth A], I [auth F]	PF17993	Haemagglutinin 70 C-terminal domain (HA70_C)	Haemagglutinin 70 C-terminal domain	This is the C-terminal domain found in hemagglutinin component such as HA70 found in Clostridium botulinum. HA is a component of the large botulinum neurotoxin complex and is critical for its oral toxicity. HA plays multiple roles in toxin penetratio ...	This is the C-terminal domain found in hemagglutinin component such as HA70 found in Clostridium botulinum. HA is a component of the large botulinum neurotoxin complex and is critical for its oral toxicity. HA plays multiple roles in toxin penetration in the gastrointestinal tract, including protection from the digestive environment, binding to the intestinal mucosal surface, and disruption of the epithelial barrier [1]. HA consists of three different proteins, designated HA70 (also known as HA3), HA33 (HA1), and HA17 (HA2) based on molecular mass [2]. HA70 consists of three domains (D1-3). The D1 and D2 domains, which adopt similar structures, mediate the trimerization of HA70 with each protomer. The D3 domain, sitting at the tip of the trimer, is composed of two similar jelly-roll-like beta-sandwich structures [3]. Furthermore, crystal structures of HA70 in a complex with alpha2,3- or alpha2,6-SiaLac (alpha2,6-sialyllactose), show that alpha2,3- and alpha2,6-SiaLac bound to the same region in the D3 domain of HA70. This domain is the D3 domain found in HA3/HA70 which has been shown to be involved in binding to carbohydrate of glycoproteins from epithelial cells in the infection process [2].	Domain
A [auth D], C, F [auth I], H	PF14200	Ricin-type beta-trefoil lectin domain-like (RicinB_lectin_2)	Ricin-type beta-trefoil lectin domain-like		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, J	Cadherin-1	protein binding binding alpha-catenin binding cytoskeletal protein binding protein phosphatase binding phosphatase binding enzyme binding molecular adaptor activity identical protein binding cation binding ion binding calcium ion binding metal ion binding small molecule binding protein binding binding alpha-catenin binding cytoskeletal protein binding protein phosphatase binding phosphatase binding enzyme binding molecular adaptor activity identical protein binding cation binding ion binding calcium ion binding metal ion binding small molecule binding protein domain specific binding beta-catenin binding	developmental process ear development sensory organ development inner ear development cochlea development animal organ development anatomical structure development cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling canonical Wnt signaling pathway developmental process ear development sensory organ development inner ear development cochlea development animal organ development anatomical structure development cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling canonical Wnt signaling pathway biological regulation cell communication cellular process signal transduction Wnt signaling pathway establishment of skin barrier epithelium development skin development skin epidermis development epidermis development tissue development regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process negative regulation of signaling regulation of canonical Wnt signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication negative regulation of Wnt signaling pathway negative regulation of cellular process regulation of signaling regulation of Wnt signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway regulation of response to stimulus regulation of cell communication localization protein localization to cell periphery cellular localization protein localization to plasma membrane macromolecule localization intracellular protein localization localization within membrane protein localization to membrane cellular component organization organelle organization actin cytoskeleton organization actin filament-based process cellular component organization or biogenesis cytoskeleton organization multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development bicellular tight junction assembly tight junction organization apical junction assembly cellular component biogenesis cell junction organization cellular component assembly cell junction assembly tight junction assembly cell-cell junction assembly cell-cell junction organization reproductive system development oviduct development oviduct epithelium development tube development reproductive process uterus development developmental process involved in reproduction reproductive structure development uterine epithelium development system development cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical cellular response to chemical stimulus response to chemical response to amino acid digestive system development cellular developmental process intestinal epithelial cell differentiation intestinal epithelial cell development cell development digestive tract development epithelial cell differentiation epithelial cell development columnar/cuboidal epithelial cell development cell differentiation columnar/cuboidal epithelial cell differentiation system process sensory perception nervous system process sensory perception of sound sensory perception of mechanical stimulus cell adhesion cell-cell adhesion homophilic cell-cell adhesion negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation calcium-dependent cell-cell adhesion salivary gland cavitation gland development salivary gland development tube formation anatomical structure morphogenesis tube morphogenesis gland morphogenesis salivary gland morphogenesis anatomical structure formation involved in morphogenesis tube lumen cavitation animal organ morphogenesis exocrine system development regulation of localization regulation of protein localization negative regulation of protein localization to plasma membrane regulation of protein localization to membrane negative regulation of protein localization regulation of protein localization to cell periphery negative regulation of protein localization to membrane regulation of cellular localization negative regulation of protein localization to cell periphery regulation of protein localization to plasma membrane protein localization to cell surface regulation of protein localization to cell surface cell morphogenesis epithelial cell morphogenesis positive regulation of cell adhesion regulation of cell adhesion positive regulation of biological process positive regulation of cell-cell adhesion regulation of cell-cell adhesion positive regulation of cellular process desmosome organization desmosome assembly regulation of cell motility neuron migration nervous system development regulation of neuron migration generation of neurons neurogenesis regulation of locomotion regulation of cell migration cell migration cell motility locomotion trophectodermal cell differentiation blastocyst formation blastocyst development cell-cell adhesion mediated by cadherin multi-multicellular organism process female pregnancy embryo implantation multi-organism reproductive process positive regulation of protein localization placenta development maternal process involved in female pregnancy multicellular organismal reproductive process maternal placenta development decidualization regulation of protein maturation negative regulation of proteolysis negative regulation of protein maturation regulation of primary metabolic process protein maturation regulation of proteolysis proteolysis protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of protein metabolic process negative regulation of metabolic process primary metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of protein processing protein processing negative regulation of protein processing regulation of developmental process branching involved in salivary gland morphogenesis regulation of branching involved in salivary gland morphogenesis regulation of morphogenesis of an epithelium regulation of multicellular organismal process regulation of anatomical structure morphogenesis regulation of morphogenesis of a branching structure regulation of animal organ morphogenesis morphogenesis of an epithelium tissue morphogenesis morphogenesis of a branching structure morphogenesis of a branching epithelium	cellular anatomical structure apical part of cell cell-cell junction anchoring junction cell junction cell periphery basal part of cell membrane plasma membrane basal plasma membrane plasma membrane region basolateral plasma membrane protein-containing complex extrinsic component of plasma membrane cellular anatomical structure apical part of cell cell-cell junction anchoring junction cell junction cell periphery basal part of cell membrane plasma membrane basal plasma membrane plasma membrane region basolateral plasma membrane protein-containing complex extrinsic component of plasma membrane catenin complex plasma membrane protein complex membrane protein complex extrinsic component of membrane intracellular anatomical structure cytoplasm membrane raft plasma membrane raft caveola membrane microdomain flotillin complex apical junction complex adherens junction membrane-bounded organelle intracellular organelle Golgi apparatus organelle intracellular membrane-bounded organelle endomembrane system desmosome cell projection actin-based cell projection microvillus plasma membrane bounded cell projection axon neuron projection main axon node of Ranvier cell surface compact myelin myelin sheath Schmidt-Lanterman incisure endosome intracellular vesicle cytoplasmic vesicle vesicle lateral loop synapse axon terminus presynapse distal axon neuron projection terminus
D [auth A], I [auth F]	Hemagglutinin component HA70	-	-	cellular anatomical structure extracellular region
B, G	Hemagglutinin component HA17	-	-	-
A [auth D], C, F [auth I], H	Hemagglutinin component HA33	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, J	IPR014868	Cadherin prodomain	Domain
E, J	IPR027397	Catenin binding domain superfamily	Homologous Superfamily
E, J	IPR015919	Cadherin-like superfamily	Homologous Superfamily
E, J	IPR039808	Cadherin	Family
E, J	IPR002126	Cadherin-like	Domain
E, J	IPR000233	Cadherin, Y-type LIR-motif	Domain
E, J	IPR020894	Cadherin conserved site	Conserved Site
D [auth A], I [auth F]	IPR003897	Clostridium enterotoxin	Family
D [auth A], I [auth F]	IPR040597	Hemagglutinin component HA-70, C-terminal	Domain
B, G	IPR035992	Ricin B-like lectins	Homologous Superfamily
B, G	IPR008903	Hemagglutinin component HA-17	Family
A [auth D], C, F [auth I], H	IPR035992	Ricin B-like lectins	Homologous Superfamily
A [auth D], C, F [auth I], H	IPR000772	Ricin B, lectin domain	Domain

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.