6G5K | pdb_00006g5k

Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with human synaptotagmin 1

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

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)
C [auth B]	SCOP2B Superfamily	STI-like	8042038	3000715	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041452	3000120	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	e6g5kA1	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	e6g5kA2	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 [auth B]	Toxin_R_bind_N	e6g5kB2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Toxin_R_bind_N	ECOD (1.6)
C [auth B]	Toxin_R_bind_C	e6g5kB1	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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C], D [auth 33]	Synaptotagmin-1	binding phospholipid binding lipid binding calcium-dependent phospholipid binding molecular sensor activity calcium ion sensor activity molecular function regulator activity metal ion sensor activity protein binding calmodulin binding SNARE binding syntaxin binding syntaxin-3 binding identical protein binding binding phospholipid binding lipid binding calcium-dependent phospholipid binding molecular sensor activity calcium ion sensor activity molecular function regulator activity metal ion sensor activity protein binding calmodulin binding SNARE binding syntaxin binding syntaxin-3 binding identical protein binding modified amino acid binding ion binding anion binding phosphatidylserine binding small molecule binding clathrin binding cation binding calcium ion binding metal ion binding syntaxin-1 binding protein heterodimerization activity protein dimerization activity molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity phosphatidylinositol-4,5-bisphosphate binding phosphatidylinositol bisphosphate binding phosphatidylinositol phosphate binding phosphatidylinositol binding calcium-dependent protein binding low-density lipoprotein particle receptor binding signaling receptor binding lipoprotein particle receptor binding	positive regulation of cell communication regulation of localization regulated exocytosis regulation of cellular process synaptic vesicle cycle positive regulation of neurotransmitter secretion synaptic vesicle exocytosis positive regulation of calcium ion-dependent exocytosis of neurotransmitter vesicle-mediated transport cell communication vesicle-mediated transport in synapse localization positive regulation of regulated secretory pathway establishment of localization in cell positive regulation of cell communication regulation of localization regulated exocytosis regulation of cellular process synaptic vesicle cycle positive regulation of neurotransmitter secretion synaptic vesicle exocytosis positive regulation of calcium ion-dependent exocytosis of neurotransmitter vesicle-mediated transport cell communication vesicle-mediated transport in synapse localization positive regulation of regulated secretory pathway establishment of localization in cell calcium ion-regulated exocytosis of neurotransmitter trans-synaptic signaling regulation of biological process positive regulation of neurotransmitter transport neurotransmitter secretion regulation of synaptic vesicle exocytosis positive regulation of synaptic transmission neurotransmitter transport establishment of localization regulation of secretion signal release from synapse exocytosis regulation of trans-synaptic signaling cellular localization regulation of calcium ion-dependent exocytosis of neurotransmitter transport signaling modulation of chemical synaptic transmission regulation of calcium ion-dependent exocytosis positive regulation of biological process positive regulation of secretion by cell positive regulation of exocytosis regulation of regulated secretory pathway synaptic signaling secretion by cell regulation of secretion by cell positive regulation of secretion signal release positive regulation of cellular process calcium-ion regulated exocytosis regulation of signaling positive regulation of calcium ion-dependent exocytosis positive regulation of synaptic vesicle exocytosis secretion regulation of transport regulation of neurotransmitter transport biological regulation export from cell cell-cell signaling regulation of vesicle-mediated transport chemical synaptic transmission positive regulation of transport regulation of neurotransmitter secretion anterograde trans-synaptic signaling regulation of exocytosis regulation of cell communication cellular process positive regulation of signaling cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular component organization or biogenesis protein heterooligomerization cellular response to stimulus cellular response to metal ion cellular response to chemical stimulus response to stimulus response to metal ion response to chemical cellular response to calcium ion response to calcium ion positive regulation of organelle organization membrane fusion vesicle organization 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 positive regulation of synaptic vesicle membrane organization regulation of organelle organization organelle fusion positive regulation of vesicle fusion vesicle fusion regulation of cellular component organization positive regulation of cellular component organization organelle membrane fusion calcium-dependent activation of synaptic vesicle fusion regulation of vesicle fusion membrane organization regulation of synaptic vesicle fusion to presynaptic active zone membrane synaptic vesicle fusion to presynaptic active zone membrane organelle organization synaptic vesicle membrane organization exocytic process organelle localization by membrane tethering organelle localization vesicle docking membrane docking 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 cell differentiation anatomical structure development positive regulation of developmental growth system development developmental process nervous system development developmental growth involved in morphogenesis generation of neurons positive regulation of dendrite extension cellular developmental process 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 monoamine transport nitrogen compound transport regulation of catecholamine secretion organic hydroxy compound transport dopamine transport positive regulation of amine transport catecholamine transport positive regulation of catecholamine secretion dopamine secretion positive regulation of dopamine secretion catecholamine secretion amine transport regulation of amine transport regulation of dopamine secretion spontaneous synaptic transmission spontaneous neurotransmitter secretion synchronous neurotransmitter secretion synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic fast, calcium ion-dependent exocytosis of neurotransmitter organelle assembly membraneless organelle assembly detection of stimulus detection of chemical stimulus detection of calcium ion	cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane presynapse presynaptic active zone membrane-bounded organelle intracellular anatomical structure cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane presynapse presynaptic active zone membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane clathrin-sculpted glutamate transport vesicle clathrin-sculpted vesicle transport vesicle membrane endomembrane system clathrin-sculpted glutamate transport vesicle membrane transport vesicle presynaptic membrane dense core granule secretory granule secretory vesicle clathrin-sculpted gamma-aminobutyric acid transport vesicle clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane glutamatergic synapse cell projection neuron projection plasma membrane bounded cell projection Golgi apparatus synaptic vesicle synaptic vesicle membrane exocytic vesicle membrane exocytic vesicle axon clathrin-sculpted acetylcholine transport vesicle membrane clathrin-sculpted acetylcholine transport vesicle clathrin-sculpted monoamine transport vesicle clathrin-sculpted monoamine transport vesicle membrane presynaptic cytosol cytosol neuron to neuron synapse hippocampal mossy fiber to CA3 synapse neuron projection terminus excitatory synapse postsynaptic density postsynaptic specialization asymmetric synapse chromaffin granule membrane chromaffin granule secretory granule membrane postsynaptic cytosol
A, C [auth B]	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 [auth C], D [auth 33]	IPR000008	C2 domain	Domain
B [auth C], D [auth 33]	IPR001565	Synaptotagmin	Domain
B [auth C], D [auth 33]	IPR035892	C2 domain superfamily	Homologous Superfamily
A, C [auth B]	IPR000395	Botulinum/Tetanus toxin, catalytic chain	Domain
A, C [auth B]	IPR012928	Clostridium neurotoxin, receptor binding N-terminal	Domain
A, C [auth B]	IPR012500	Clostridium neurotoxin, translocation	Domain
A, C [auth B]	IPR011065	Kunitz inhibitor STI-like superfamily	Homologous Superfamily
A, C [auth B]	IPR013104	Clostridium neurotoxin, receptor-binding C-terminal	Domain
A, C [auth B]	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, C [auth B]	IPR036248	Clostridium neurotoxin, translocation domain	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth C], D [auth 33]	Pharos: P21579	peripheral arterial disease plasma cell myeloma acute myeloid leukemia atypical teratoid rhabdoid tumor glioblastoma lung cancer malignant glioma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Pick disease primitive neuroectodermal tumor adenoma bladder exstrophy interstitial cystitis lung carcinoma peripheral arterial disease plasma cell myeloma acute myeloid leukemia atypical teratoid rhabdoid tumor glioblastoma lung cancer malignant glioma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Pick disease primitive neuroectodermal tumor adenoma bladder exstrophy interstitial cystitis lung carcinoma malignant mesothelioma oligodendroglioma Parkinson disease pilocytic astrocytoma subependymal giant cell astrocytoma astrocytic tumor breast cancer large cell medulloblastoma malignant ependymoma medulloblastoma ovarian cancer

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.