4JRA | pdb_00004jra

CRYSTAL STRUCTURE OF THE BOTULINUM NEUROTOXIN A RECEPTOR-BINDING DOMAIN IN COMPLEX WITH THE LUMINAL DOMAIN Of 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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4jraa1	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	d4jraa2	All beta proteins	beta-Trefoil	STI-like	Clostridium neurotoxins, C-terminal domain	automated matches	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
B	d4jrab1	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)
B	d4jrab2	All beta proteins	beta-Trefoil	STI-like	Clostridium neurotoxins, C-terminal domain	automated matches	(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	STI-like	8042037	3000715	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041451	3000120	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041451	3000120	SCOP2B (2022-06-29)
B	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	Toxin_R_bind_N	e4jraA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Toxin_R_bind_N	ECOD (1.6)
A	Toxin_R_bind_C	e4jraA2	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: Toxin_R_bind_C	ECOD (1.6)
B	Toxin_R_bind_N	e4jraB1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Toxin_R_bind_N	ECOD (1.6)
B	Toxin_R_bind_C	e4jraB2	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: Toxin_R_bind_C	ECOD (1.6)
C	Pentapeptide_4	e4jraC1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Pentapeptide repeats (From Topology)	T: Pentapeptide repeats	F: Pentapeptide_4	ECOD (1.6)
D	Pentapeptide_4	e4jraD1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Pentapeptide repeats (From Topology)	T: Pentapeptide repeats	F: Pentapeptide_4	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)
B	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
C	2.160.20.80	Mainly Beta	3 Solenoid	Pectate Lyase C-like	E3 ubiquitin-protein ligase SopA	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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 tra ...	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 domain 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, B	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 tran ...	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 domain 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
C, D	PF13599	Pentapeptide repeat region (Pentapeptide_4)	Pentapeptide repeat region	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	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	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure membrane extracellular region host cell plasma membrane host cellular component host cell part host cell membrane other organism part host cell synapse host cell presynaptic membrane host intracellular part host cell cytoplasm host intracellular region host cell cytosol cellular anatomical structure membrane extracellular region host cell plasma membrane host cellular component host cell part host cell membrane other organism part host cell synapse host cell presynaptic membrane host intracellular part host cell cytoplasm host intracellular region host cell cytosol host cell cytoplasm part host intracellular membrane-bounded organelle host intracellular organelle host cell cytoplasmic vesicle
C, D	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	cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle intracellular anatomical structure synapse intracellular vesicle transport vesicle membrane endomembrane system intracellular organelle presynapse bounding membrane of organelle cytoplasmic vesicle cell periphery cellular anatomical structure plasma membrane membrane 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 exocytic vesicle membrane 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, B	IPR000395	Botulinum/Tetanus toxin, catalytic chain	Domain
A, B	IPR012928	Clostridium neurotoxin, receptor binding N-terminal	Domain
A, B	IPR012500	Clostridium neurotoxin, translocation	Domain
A, B	IPR011065	Kunitz inhibitor STI-like superfamily	Homologous Superfamily
A, B	IPR013104	Clostridium neurotoxin, receptor-binding C-terminal	Domain
A, B	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, B	IPR036248	Clostridium neurotoxin, translocation domain	Homologous Superfamily
C, D	IPR022308	Synaptic vesicle protein SV2	Family
C, D	IPR011701	Major facilitator superfamily	Family
C, D	IPR005828	Major facilitator, sugar transporter-like	Family
C, D	IPR005829	Sugar transporter, conserved site	Conserved Site
C, D	IPR055415	SV2A/B/C, luminal domain	Domain
C, D	IPR036259	MFS transporter superfamily	Homologous Superfamily
C, D	IPR020846	Major facilitator superfamily domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: Q496J9	astrocytic tumor malignant ependymoma oligodendroglioma glioblastoma malignant glioma ovarian cancer large cell medulloblastoma medulloblastoma pilocytic astrocytoma

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.