2NP0 | pdb_00002np0

Crystal structure of the Botulinum neurotoxin type B complexed with synaptotagamin-II ectodomain

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d2np0a1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Clostridium neurotoxins, the second last domain	Botulinum neurotoxin	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
A	d2np0a2	All beta proteins	beta-Trefoil	STI-like	Clostridium neurotoxins, C-terminal domain	Botulinum neurotoxin	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
A	d2np0a3	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	Clostridium neurotoxins, catalytic domain	Botulinum neurotoxin	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
A	d2np0a4	Coiled coil proteins	Antiparallel coiled-coil	Clostridium neurotoxins, 'coiled-coil' domain	Clostridium neurotoxins, 'coiled-coil' domain	Botulinum neurotoxin	(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	8042038	3000715	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041452	3000120	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8035461	3001975	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Clostridium neurotoxins, coiled-coil domain	8039657	3001677	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	e2np0A1	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	e2np0A2	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)
A	Peptidase_M27	e2np0A3	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: Peptidase_M27	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.1240.10	Alpha Beta	Alpha-Beta Complex	Zincin-like	Metalloproteases ("zincins"), catalytic domain like	CATH (4.3.0)
A	1.20.1120.10	Mainly Alpha	Up-down Bundle	Clostridium botulinum neurotoxin B, "coiled-coil" domain	Clostridium botulinum neurotoxin b, "coiled-coil" domain	CATH (4.3.0)
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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Synaptotagmin-2	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding calcium-dependent phospholipid binding phospholipid binding lipid binding protein binding SNARE binding syntaxin binding molecular sensor activity calcium ion sensor activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding calcium-dependent phospholipid binding phospholipid binding lipid binding protein binding SNARE binding syntaxin binding molecular sensor activity calcium ion sensor activity molecular function regulator activity metal ion sensor activity alcohol binding anion binding inositol 1,3,4,5 tetrakisphosphate binding modified amino acid binding phosphatidylserine binding	regulation of localization regulated exocytosis regulation of biological process regulation of cellular process regulation of calcium ion-dependent exocytosis transport secretion regulation of transport biological regulation export from cell regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport regulation of secretion regulation of regulated secretory pathway regulation of localization regulated exocytosis regulation of biological process regulation of cellular process regulation of calcium ion-dependent exocytosis transport secretion regulation of transport biological regulation export from cell regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport regulation of secretion regulation of regulated secretory pathway localization secretion by cell regulation of secretion by cell exocytosis regulation of exocytosis cellular process calcium-ion regulated exocytosis developmental process cellular developmental process cell differentiation positive regulation of organelle organization membrane fusion synaptic vesicle cycle synaptic vesicle exocytosis cell communication vesicle-mediated transport in synapse vesicle organization establishment of localization in cell positive regulation of synaptic vesicle fusion to presynaptic active zone membrane regulation of synaptic vesicle membrane organization endomembrane system organization vesicle fusion to plasma membrane trans-synaptic signaling neurotransmitter secretion neurotransmitter transport positive regulation of synaptic vesicle membrane organization regulation of organelle organization organelle fusion signal release from synapse positive regulation of vesicle fusion vesicle fusion cellular localization regulation of cellular component organization positive regulation of cellular component organization signaling organelle membrane fusion positive regulation of biological process calcium-dependent activation of synaptic vesicle fusion regulation of vesicle fusion cellular component organization synaptic signaling signal release cellular component organization or biogenesis positive regulation of cellular process membrane organization regulation of synaptic vesicle fusion to presynaptic active zone membrane cell-cell signaling synaptic vesicle fusion to presynaptic active zone membrane chemical synaptic transmission organelle organization positive regulation of transport anterograde trans-synaptic signaling synaptic vesicle membrane organization exocytic process modulation of chemical synaptic transmission regulation of signaling regulation of neurotransmitter transport regulation of synaptic vesicle exocytosis regulation of trans-synaptic signaling regulation of neurotransmitter secretion regulation of cell communication multicellular organismal process regulation of growth developmental growth cell projection organization neuron projection development regulation of cell morphogenesis positive regulation of developmental process multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis anatomical structure development positive regulation of developmental growth system development nervous system development developmental growth involved in morphogenesis generation of neurons positive regulation of dendrite extension regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis neurogenesis dendrite extension regulation of anatomical structure morphogenesis neuron projection extension regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth growth regulation of dendrite extension positive regulation of cell growth regulation of cell growth anatomical structure morphogenesis positive regulation of growth neuron development	cellular anatomical structure neuromuscular junction synapse cell junction membrane-bounded organelle intracellular anatomical structure transport vesicle intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle secretory vesicle cellular anatomical structure neuromuscular junction synapse cell junction membrane-bounded organelle intracellular anatomical structure transport vesicle intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle secretory vesicle cytoplasm vesicle exocytic vesicle cell periphery plasma membrane membrane dense core granule secretory granule transport vesicle membrane presynapse bounding membrane of organelle vesicle membrane synaptic vesicle synaptic vesicle membrane exocytic vesicle membrane cytoplasmic vesicle membrane organelle membrane axon cell projection neuron projection plasma membrane bounded cell projection chromaffin granule membrane chromaffin granule secretory granule membrane
A	Botulinum neurotoxin type B	binding lipid 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 binding lipid 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 metal ion binding small molecule binding	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure extracellular region host cellular component host cell part host cell synapse host cell membrane host cell presynaptic membrane other organism part host intracellular part host cell cytoplasm host intracellular region host cell cytosol host cell cytoplasm part host intracellular membrane-bounded organelle cellular anatomical structure extracellular region host cellular component host cell part host cell synapse host cell membrane host cell presynaptic membrane other organism part 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR000008	C2 domain	Domain
B	IPR035892	C2 domain superfamily	Homologous Superfamily
B	IPR001565	Synaptotagmin	Domain
A	IPR000395	Botulinum/Tetanus toxin, catalytic chain	Domain
A	IPR012928	Clostridium neurotoxin, receptor binding N-terminal	Domain
A	IPR012500	Clostridium neurotoxin, translocation	Domain
A	IPR011065	Kunitz inhibitor STI-like superfamily	Homologous Superfamily
A	IPR013104	Clostridium neurotoxin, receptor-binding C-terminal	Domain
A	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A	IPR036248	Clostridium neurotoxin, translocation domain	Homologous Superfamily

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.