4QD2

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)
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)
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)
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)
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)
E	d4qd2e1	All beta proteins	Immunoglobulin-like beta-sandwich	Cadherin-like	Cadherin	E-cadherin (epithelial)	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
J	d4qd2j1	All beta proteins	Immunoglobulin-like beta-sandwich	Cadherin-like	Cadherin	E-cadherin (epithelial)	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	Cadherin-like	8055233	3002049	SCOP2B (2022-06-29)
J	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)
A [auth D]	PF05588	e4qd2D2	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF05588	ECOD (1.6)
A [auth D]	PF14200	e4qd2D1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF14200	ECOD (1.6)
C	PF05588	e4qd2C2	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF05588	ECOD (1.6)
C	PF14200	e4qd2C1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF14200	ECOD (1.6)
F [auth I]	PF05588	e4qd2I2	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF05588	ECOD (1.6)
F [auth I]	PF14200	e4qd2I1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF14200	ECOD (1.6)
H	PF05588	e4qd2H2	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF05588	ECOD (1.6)
H	PF14200	e4qd2H1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF14200	ECOD (1.6)
B	PF05588	e4qd2B1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF05588	ECOD (1.6)
G	PF05588	e4qd2G1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF05588	ECOD (1.6)
D [auth A]	PF17993	e4qd2A1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: PF17993	ECOD (1.6)
D [auth A]	PF03505	e4qd2A2	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF03505	ECOD (1.6)
I [auth F]	PF17993	e4qd2F1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: PF17993	ECOD (1.6)
I [auth F]	PF03505	e4qd2F2	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF03505	ECOD (1.6)
E	PF00028	e4qd2E2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF00028	ECOD (1.6)
J	PF00028	e4qd2J2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF00028	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
B, G	PF05588	Clostridium botulinum HA-17 domain (Botulinum_HA-17)	Clostridium botulinum HA-17 domain	This family consists of several Clostridium botulinum hemagglutinin (HA) subcomponents. Clostridium botulinum type D strain 4947 produces two different sizes of progenitor toxins (M and L) as intact forms without proteolytic processing. The M toxin i ...	This family consists of several Clostridium botulinum hemagglutinin (HA) subcomponents. Clostridium botulinum type D strain 4947 produces two different sizes of progenitor toxins (M and L) as intact forms without proteolytic processing. The M toxin is composed of neurotoxin (NT) and nontoxic-nonhemagglutinin (NTNHA), whereas the L toxin is composed of the M toxin and hemagglutinin (HA) subcomponents (HA-70, HA-17, and HA-33) [1].	Domain
D [auth A], I [auth F]	PF03505	Clostridium enterotoxin (Clenterotox)	Clostridium enterotoxin	-	Family
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
E, J	PF00028	Cadherin domain (Cadherin)	Cadherin domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D], C, F [auth I], H	Hemagglutinin component HA33	-	-	-
B, G	Hemagglutinin component HA17	-	-	-
D [auth A], I [auth F]	Hemagglutinin component HA70	-	-	extracellular region cellular anatomical entity
E, J	Cadherin-1	protein binding binding alpha-catenin binding cytoskeletal protein binding ankyrin binding protein phosphatase binding phosphatase binding enzyme binding cell adhesion molecule binding cadherin binding molecular adaptor activity protein tyrosine kinase binding kinase binding protein kinase binding protein binding binding alpha-catenin binding cytoskeletal protein binding ankyrin binding protein phosphatase binding phosphatase binding enzyme binding cell adhesion molecule binding cadherin binding molecular adaptor activity protein tyrosine kinase binding kinase binding protein kinase binding identical protein binding gamma-catenin binding cation binding ion binding calcium ion binding metal ion binding small molecule binding protein domain specific binding GTPase activating protein binding beta-catenin binding	developmental process ear development sensory organ development inner ear development cochlea development animal organ development anatomical structure development adherens junction organization cellular component organization cell junction organization cellular process cellular component organization or biogenesis cell-cell junction organization cellular response to stimulus developmental process ear development sensory organ development inner ear development cochlea development animal organ development anatomical structure development adherens junction organization cellular component organization cell junction organization cellular process cellular component organization or biogenesis cell-cell junction organization cellular response to stimulus cellular response to inorganic substance cellular response to metal ion cellular response to lithium ion response to stimulus response to inorganic substance cellular response to chemical stimulus response to lithium ion response to metal ion response to chemical regulation of biological process regulation of cellular process cell surface receptor signaling pathway signaling canonical Wnt signaling pathway biological regulation cell communication signal transduction Wnt signaling pathway axon extension multicellular organismal process regulation of growth axonogenesis regulation of cellular component size developmental growth cell projection organization negative regulation of biological process regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development multicellular organism development cell projection morphogenesis neuron differentiation negative regulation of growth neuron projection morphogenesis cell differentiation regulation of biological quality system development negative regulation of cellular component organization regulation of cell projection organization negative regulation of cell growth nervous system development developmental growth involved in morphogenesis generation of neurons negative regulation of axonogenesis negative regulation of developmental growth negative regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis regulation of axon extension regulation of nervous system development neurogenesis negative regulation of neurogenesis regulation of extent of cell growth regulation of axonogenesis negative regulation of cellular process negative regulation of nervous system development regulation of multicellular organismal process negative regulation of cell differentiation negative regulation of cell projection organization regulation of anatomical structure morphogenesis regulation of cell size neuron projection extension regulation of multicellular organismal development regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth negative regulation of developmental process growth negative regulation of axon extension axon development regulation of cell growth cell morphogenesis involved in neuron differentiation negative regulation of neuron projection development anatomical structure morphogenesis negative regulation of cell development neuron development regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size establishment of skin barrier epithelium development skin development skin epidermis development epidermis development tissue development regulation of biosynthetic process cellular biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression organic substance metabolic process biosynthetic process organic substance 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 regulation of signal transduction negative regulation of cell communication negative regulation of Wnt signaling pathway 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 protein localization localization protein localization to cell periphery cellular localization protein localization to plasma membrane cellular macromolecule localization macromolecule localization localization within membrane protein localization to membrane organelle organization actin cytoskeleton organization actin filament-based process cytoskeleton organization cellular component biogenesis cellular component assembly cell junction assembly cell-cell junction assembly regulation of localization establishment of protein localization nitrogen compound transport nucleocytoplasmic transport nuclear transport positive regulation of establishment of protein localization import into nucleus establishment of localization in cell regulation of intracellular transport positive regulation of protein localization to nucleus organic substance transport positive regulation of protein import into nucleus intracellular transport regulation of nucleocytoplasmic transport protein localization to nucleus establishment of localization establishment of protein localization to organelle positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport intracellular protein transport regulation of protein localization transport positive regulation of nucleocytoplasmic transport positive regulation of biological process regulation of protein localization to nucleus positive regulation of protein transport regulation of protein import into nucleus protein import into nucleus positive regulation of intracellular transport positive regulation of cellular process regulation of transport regulation of establishment of protein localization regulation of protein transport positive regulation of transport regulation of cellular localization protein transport protein localization to organelle embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development regulation of cell adhesion negative regulation of cell adhesion cell adhesion cell-cell adhesion negative regulation of cell-cell adhesion regulation of cell-cell adhesion bicellular tight junction assembly tight junction organization apical junction assembly tight junction assembly 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 cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to organic substance response to amino acid negative regulation of locomotion regulation of cell motility regulation of locomotion regulation of cell migration negative regulation of cell motility cell migration cell motility negative regulation of cell migration locomotion organonitrogen compound metabolic process primary metabolic process protein metabolic process digestive system development intestinal epithelial cell differentiation intestinal epithelial cell development digestive tract development epithelial cell differentiation epithelial cell development columnar/cuboidal epithelial cell development columnar/cuboidal epithelial cell differentiation system process sensory perception nervous system process sensory perception of sound sensory perception of mechanical stimulus cell-cell adhesion via plasma-membrane adhesion molecules homophilic cell adhesion via plasma membrane adhesion molecules 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 synapse organization synapse assembly calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules salivary gland cavitation gland development salivary gland development tube formation tube morphogenesis gland morphogenesis salivary gland morphogenesis anatomical structure formation involved in morphogenesis tube lumen cavitation animal organ morphogenesis exocrine system development 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 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 epithelial cell morphogenesis positive regulation of cell adhesion positive regulation of cell-cell adhesion neuron migration regulation of neuron migration 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 catabolic process modulation of chemical synaptic transmission macromolecule catabolic process regulation of protein catabolic process at postsynapse, modulating synaptic transmission regulation of primary metabolic process synaptic signaling postsynaptic modulation of chemical synaptic transmission organonitrogen compound catabolic process trans-synaptic signaling regulation of protein metabolic process cell-cell signaling protein catabolic process regulation of catabolic process chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling organic substance catabolic process regulation of protein catabolic process 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 negative regulation of cellular metabolic process protein maturation regulation of proteolysis proteolysis negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of metabolic process negative regulation of cellular biosynthetic 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 cellular response to nitrogen compound response to alcohol response to organonitrogen compound response to endogenous stimulus cellular response to organic cyclic compound response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to alcohol cellular response to organonitrogen compound response to indole-3-methanol cellular response to indole-3-methanol cellular response to organic substance response to organic cyclic compound positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process branching involved in salivary gland morphogenesis regulation of branching involved in salivary gland morphogenesis regulation of morphogenesis of an epithelium 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	cell projection cell leading edge cellular anatomical entity plasma membrane bounded cell projection lamellipodium membrane apical part of cell cell-cell junction anchoring junction cell junction intracellular organelle intracellular anatomical structure cytoskeleton organelle cell projection cell leading edge cellular anatomical entity plasma membrane bounded cell projection lamellipodium membrane apical part of cell cell-cell junction anchoring junction cell junction intracellular organelle intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle actin cytoskeleton non-membrane-bounded organelle cell periphery basal part of cell 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 cytoplasm membrane raft plasma membrane raft caveola membrane microdomain flotillin complex synapse glutamatergic synapse apical junction complex adherens junction membrane-bounded organelle Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system trans-Golgi network actin-based cell projection microvillus perinuclear region of cytoplasm axon neuron projection postsynapse main axon node of Ranvier cell surface compact myelin myelin sheath Schmidt-Lanterman incisure endosome intracellular vesicle cytoplasmic vesicle vesicle lateral plasma membrane lateral loop axon terminus presynapse distal axon neuron projection terminus cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
B, G	IPR035992	Ricin B-like lectins	Homologous Superfamily
B, G	IPR008903	Hemagglutinin component HA-17	Family
D [auth A], I [auth F]	IPR003897	Clostridium enterotoxin	Family
D [auth A], I [auth F]	IPR040597	Hemagglutinin component HA-70, C-terminal	Domain
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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.