8C5H | pdb_00008c5h

NbSyt1 anti-(rat Synaptotagmin-1) nanobody bound to target cytosolic domain of Synaptotagmin-1

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth S]	SCOP2B Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8086451	3000965	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 S]	Pico_P2A	e8c5hS1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Pico_P2A	ECOD (v294.1)
B [auth N]	Pico_P2A	e8c5hN1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Pico_P2A	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth N]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth N]	Heavy Chain	IGHV3	-	synaptotagmin-1	SAbDab (2026-04-10)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth S]	PF00168	C2 domain (C2)	C2 domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth S]	Synaptotagmin-1	protein binding binding SNARE binding syntaxin binding phospholipid binding lipid binding calcium-dependent phospholipid binding molecular sensor activity calcium ion sensor activity molecular function regulator activity metal ion sensor activity calmodulin binding syntaxin-3 binding identical protein binding protein binding binding SNARE binding syntaxin binding phospholipid binding lipid binding calcium-dependent phospholipid binding molecular sensor activity calcium ion sensor activity molecular function regulator activity metal ion sensor activity calmodulin 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 calcium-dependent protein binding low-density lipoprotein particle receptor binding signaling receptor binding lipoprotein particle receptor binding	regulation of localization regulation of cellular component organization regulation of cellular process transport membrane fusion organelle membrane fusion regulation of vesicle fusion vesicle-mediated transport vesicle organization cellular component organization localization cellular component organization or biogenesis membrane organization regulation of biological process regulation of localization regulation of cellular component organization regulation of cellular process transport membrane fusion organelle membrane fusion regulation of vesicle fusion vesicle-mediated transport vesicle organization cellular component organization localization cellular component organization or biogenesis membrane organization regulation of biological process regulation of transport biological regulation regulation of vesicle-mediated transport establishment of localization regulation of organelle organization organelle fusion organelle organization cellular process vesicle fusion regulated exocytosis secretion export from cell secretion by cell exocytosis calcium-ion regulated exocytosis response to stimulus response to metal ion response to chemical response to calcium ion import into cell endocytosis regulation of endocytosis positive regulation of cell communication synaptic vesicle cycle positive regulation of neurotransmitter secretion synaptic vesicle exocytosis positive regulation of calcium ion-dependent exocytosis of neurotransmitter cell communication vesicle-mediated transport in synapse positive regulation of regulated secretory pathway establishment of localization in cell calcium ion-regulated exocytosis of neurotransmitter trans-synaptic signaling positive regulation of neurotransmitter transport neurotransmitter secretion regulation of synaptic vesicle exocytosis positive regulation of synaptic transmission neurotransmitter transport regulation of secretion signal release from synapse regulation of trans-synaptic signaling cellular localization regulation of calcium ion-dependent exocytosis of neurotransmitter 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 regulation of secretion by cell positive regulation of secretion signal release positive regulation of cellular process regulation of signaling positive regulation of calcium ion-dependent exocytosis positive regulation of synaptic vesicle exocytosis regulation of neurotransmitter transport cell-cell signaling chemical synaptic transmission positive regulation of transport regulation of neurotransmitter secretion anterograde trans-synaptic signaling regulation of exocytosis regulation of cell communication positive regulation of signaling cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein heterooligomerization transmembrane transport xenobiotic transmembrane transport xenobiotic transport positive regulation of organelle organization positive regulation of cellular component organization positive regulation of vesicle fusion cellular response to stimulus cellular response to metal ion cellular response to chemical stimulus cellular response to calcium ion 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 calcium-dependent activation of synaptic vesicle fusion regulation of synaptic vesicle fusion to presynaptic active zone membrane synaptic vesicle fusion to presynaptic active zone membrane synaptic vesicle membrane organization exocytic process multicellular organismal process regulation of postsynaptic membrane potential system process chemical synaptic transmission, postsynaptic signal transduction regulation of biological quality cell surface receptor signaling pathway nervous system process inhibitory postsynaptic potential regulation of membrane potential regulation of calcium-dependent activation of synaptic vesicle fusion organelle localization by membrane tethering organelle localization vesicle docking membrane docking 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 synaptic vesicle recycling monoamine transport nitrogen compound transport regulation of catecholamine secretion organic hydroxy compound transport dopamine transport catecholamine transport dopamine secretion catecholamine secretion amine transport regulation of amine transport regulation of dopamine secretion positive regulation of amine transport positive regulation of catecholamine secretion positive regulation of dopamine secretion spontaneous synaptic transmission spontaneous neurotransmitter secretion synchronous neurotransmitter secretion calcium activated phospholipid scrambling phospholipid translocation lipid localization phospholipid transport lipid transport lipid translocation regulation of membrane lipid distribution plasma membrane phospholipid scrambling plasma membrane organization macromolecule localization organophosphate ester transport negative regulation of biological process negative regulation of transport negative regulation of neurotransmitter transport negative regulation of secretion negative regulation of cellular process negative regulation of secretion by cell negative regulation of neurotransmitter secretion establishment of protein localization establishment of protein localization to membrane localization within membrane intracellular protein localization protein insertion into membrane synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic vesicle localization establishment of organelle localization establishment of vesicle localization vesicle targeting 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 presynaptic membrane membrane-bounded organelle cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane presynapse presynaptic active zone presynaptic membrane membrane-bounded organelle intracellular anatomical structure dense core granule intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle glutamatergic synapse cell projection neuron projection plasma membrane bounded cell projection Golgi apparatus transport vesicle membrane bounding membrane of organelle vesicle membrane synaptic vesicle synaptic vesicle membrane transport vesicle exocytic vesicle membrane cytoplasmic vesicle membrane organelle membrane exocytic vesicle axon axon terminus distal axon terminal bouton neuron projection terminus presynaptic cytosol cytosol neuron to neuron synapse hippocampal mossy fiber to CA3 synapse excitatory synapse postsynaptic density postsynaptic specialization asymmetric synapse chromaffin granule membrane chromaffin granule secretory granule membrane postsynaptic cytosol
B [auth N]	NbSyt1 nanobody	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth S]	IPR000008	C2 domain	Domain
A [auth S]	IPR001565	Synaptotagmin	Domain
A [auth S]	IPR035892	C2 domain superfamily	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.

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