5JMC

Receptor binding domain of Botulinum neurotoxin A in complex with rat SV2C

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	d5jmca1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Clostridium neurotoxins, the second last domain	automated matches	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
A	d5jmca2	All beta proteins	beta-Trefoil	STI-like	Clostridium neurotoxins, C-terminal domain	automated matches	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
A	d5jmca4	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
A	d5jmca3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
C	d5jmcc1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Clostridium neurotoxins, the second last domain	automated matches	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
C	d5jmcc2	All beta proteins	beta-Trefoil	STI-like	Clostridium neurotoxins, C-terminal domain	automated matches	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
C	d5jmcc4	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
C	d5jmcc3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
G	d5jmcg1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Clostridium neurotoxins, the second last domain	automated matches	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
G	d5jmcg2	All beta proteins	beta-Trefoil	STI-like	Clostridium neurotoxins, C-terminal domain	automated matches	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
G	d5jmcg4	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
G	d5jmcg3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
E	d5jmce1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Clostridium neurotoxins, the second last domain	automated matches	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
E	d5jmce2	All beta proteins	beta-Trefoil	STI-like	Clostridium neurotoxins, C-terminal domain	automated matches	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
E	d5jmce4	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
E	d5jmce3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041451	3000120	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	STI-like	8042037	3000715	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041451	3000120	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	STI-like	8042037	3000715	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	STI-like	8042037	3000715	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041451	3000120	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041451	3000120	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	STI-like	8042037	3000715	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	PF07953	e5jmcA2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: PF07953	ECOD (1.6)
A	PF07951	e5jmcA1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF07951	ECOD (1.6)
C	PF07953	e5jmcC1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: PF07953	ECOD (1.6)
C	PF07951	e5jmcC2	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF07951	ECOD (1.6)
G	PF07953	e5jmcG1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: PF07953	ECOD (1.6)
G	PF07951	e5jmcG2	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF07951	ECOD (1.6)
E	PF07953	e5jmcE2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: PF07953	ECOD (1.6)
E	PF07951	e5jmcE1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF07951	ECOD (1.6)
D	PF13599	e5jmcD1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Pentapeptide repeats (From Topology)	T: Pentapeptide repeats	F: PF13599	ECOD (1.6)
F	PF13599	e5jmcF1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Pentapeptide repeats (From Topology)	T: Pentapeptide repeats	F: PF13599	ECOD (1.6)
H	PF13599	e5jmcH1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Pentapeptide repeats (From Topology)	T: Pentapeptide repeats	F: PF13599	ECOD (1.6)
B	PF13599	e5jmcB1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Pentapeptide repeats (From Topology)	T: Pentapeptide repeats	F: PF13599	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
A	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
C	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
G	2.60.120.200	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)
E	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
E	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
D	2.160.20.80	Mainly Beta	3 Solenoid	Pectate Lyase C-like	E3 ubiquitin-protein ligase SopA	CATH (4.3.0)
F	2.160.20.80	Mainly Beta	3 Solenoid	Pectate Lyase C-like	E3 ubiquitin-protein ligase SopA	CATH (4.3.0)
H	2.160.20.80	Mainly Beta	3 Solenoid	Pectate Lyase C-like	E3 ubiquitin-protein ligase SopA	CATH (4.3.0)
B	2.160.20.80	Mainly Beta	3 Solenoid	Pectate Lyase C-like	E3 ubiquitin-protein ligase SopA	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF07951	Clostridium neurotoxin, C-terminal receptor binding (Toxin_R_bind_C)	Clostridium neurotoxin, C-terminal receptor binding	The Clostridium neurotoxin family is composed of tetanus neurotoxins and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein. The N-terminal catalytic domain (Pfam:PF01742), the central tr ...	The Clostridium neurotoxin family is composed of tetanus neurotoxins and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein. The N-terminal catalytic domain (Pfam:PF01742), the central translocation domains and two receptor binding domains [1]. This domains is the C-terminal receptor binding domain, which adopts a modified beta-trefoil fold with a six stranded beta-barrel and a beta-hairpin triplet capping the domain [1]. The first step in the intoxication process is a binding event between this domains and the pre-synaptic nerve ending [1].	Domain
A, C, E, G	PF07953	Clostridium neurotoxin, N-terminal receptor binding (Toxin_R_bind_N)	Clostridium neurotoxin, N-terminal receptor binding	The Clostridium neurotoxin family is composed of tetanus neurotoxin and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein. The N-terminal catalytic domain (Pfam:PF01742), the central tra ...	The Clostridium neurotoxin family is composed of tetanus neurotoxin and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein. The N-terminal catalytic domain (Pfam:PF01742), the central translocation domains and two receptor binding domains [1]. This domains is the N-terminal receptor binding domain,which is comprised of two seven-stranded beta-sheets sandwiched together to form a jelly role motif [1]. The role of this domain in receptor binding appears to be indirect.	Domain
B, D, F, H	PF13599	Pentapeptide repeats (9 copies) (Pentapeptide_4)	Pentapeptide repeats (9 copies)	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	Botulinum neurotoxin type A	macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity peptidase activity catalytic activity, acting on a protein metalloendopeptidase activity hydrolase activity metallopeptidase activity catalytic activity endopeptidase activity toxin activity cation binding macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity peptidase activity catalytic activity, acting on a protein metalloendopeptidase activity hydrolase activity metallopeptidase activity catalytic activity endopeptidase activity toxin activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	membrane cellular anatomical entity extracellular region host cell plasma membrane host cellular component host cell part host cell membrane host cell synapse host cell presynaptic membrane host intracellular part host cell cytoplasm host intracellular region host cell cytosol host cell cytoplasm part membrane cellular anatomical entity extracellular region host cell plasma membrane host cellular component host cell part host cell membrane host cell synapse host cell presynaptic membrane host intracellular part host cell cytoplasm host intracellular region host cell cytosol host cell cytoplasm part host cell cytoplasmic vesicle host intracellular membrane-bounded organelle host intracellular organelle
B, D, F, H	Synaptic vesicle glycoprotein 2C	transporter activity transmembrane transporter activity	localization transport neurotransmitter transport establishment of localization trans-synaptic signaling synaptic signaling regulation of biological process signaling anterograde trans-synaptic signaling biological regulation cell-cell signaling cellular process chemical synaptic transmission cell communication localization transport neurotransmitter transport establishment of localization trans-synaptic signaling synaptic signaling regulation of biological process signaling anterograde trans-synaptic signaling biological regulation cell-cell signaling cellular process chemical synaptic transmission cell communication regulation of localization cellular localization regulated exocytosis regulation of cellular process modulation of chemical synaptic transmission synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport vesicle-mediated transport in synapse regulation of regulated secretory pathway regulation of secretion by cell secretion by cell signal release establishment of localization in cell regulation of signaling neurotransmitter secretion regulation of transport secretion regulation of neurotransmitter transport regulation of synaptic vesicle exocytosis export from cell regulation of vesicle-mediated transport regulation of secretion signal release from synapse regulation of trans-synaptic signaling exocytosis regulation of neurotransmitter secretion regulation of exocytosis regulation of cell communication	membrane-bounded organelle intracellular anatomical structure synapse intracellular vesicle transport vesicle membrane endomembrane system intracellular organelle presynapse bounding membrane of organelle cytoplasmic vesicle vesicle membrane synaptic vesicle synaptic vesicle membrane cell junction membrane-bounded organelle intracellular anatomical structure synapse intracellular vesicle transport vesicle membrane endomembrane system intracellular organelle presynapse bounding membrane of organelle cytoplasmic vesicle vesicle membrane synaptic vesicle synaptic vesicle membrane cell junction vesicle transport vesicle membrane exocytic vesicle membrane cellular anatomical entity intracellular membrane-bounded organelle cytoplasmic vesicle membrane organelle secretory vesicle cytoplasm organelle membrane exocytic vesicle dopaminergic synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR000395	Botulinum/Tetanus toxin, catalytic chain	Domain
A, C, E, G	IPR012928	Clostridium neurotoxin, receptor binding N-terminal	Domain
A, C, E, G	IPR012500	Clostridium neurotoxin, translocation	Domain
A, C, E, G	IPR011065	Kunitz inhibitor STI-like superfamily	Homologous Superfamily
A, C, E, G	IPR013104	Clostridium neurotoxin, receptor-binding C-terminal	Domain
A, C, E, G	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, C, E, G	IPR036248	Clostridium neurotoxin, translocation domain	Homologous Superfamily
B, D, F, H	IPR022308	Synaptic vesicle protein SV2	Family
B, D, F, H	IPR011701	Major facilitator superfamily	Family
B, D, F, H	IPR005828	Major facilitator, sugar transporter-like	Family
B, D, F, H	IPR005829	Sugar transporter, conserved site	Conserved Site
B, D, F, H	IPR001646	Pentapeptide repeat	Repeat
B, D, F, H	IPR036259	MFS transporter superfamily	Homologous Superfamily
B, D, F, H	IPR020846	Major facilitator superfamily 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 R01GM133198.