3HN8 | pdb_00003hn8

Crystal structure of synaptotagmin

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8040723	3000965	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8040722	3000965	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8040722	3000965	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8040723	3000965	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8040722	3000965	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8040723	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)
C	RVP	e3hn8C1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)
B	RVP	e3hn8B1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)
A	Arginase	e3hn8A1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: HTH	T: winged helix domain	F: Arginase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.60.40.150	Mainly Beta	Sandwich	Immunoglobulin-like	C2 domain	CATH (4.3.0)
B	2.60.40.150	Mainly Beta	Sandwich	Immunoglobulin-like	C2 domain	CATH (4.3.0)
A	2.60.40.150	Mainly Beta	Sandwich	Immunoglobulin-like	C2 domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	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, B, C	Synaptotagmin-3	clathrin binding protein binding binding cation binding ion binding calcium ion binding metal ion binding small molecule binding SNARE binding syntaxin binding protein heterodimerization activity protein dimerization activity phosphatidylinositol-4,5-bisphosphate binding anion binding clathrin binding protein binding binding cation binding ion binding calcium ion binding metal ion binding small molecule binding SNARE binding syntaxin binding protein heterodimerization activity protein dimerization activity phosphatidylinositol-4,5-bisphosphate binding anion binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding calcium-dependent phospholipid binding identical protein binding protein homodimerization activity molecular sensor activity calcium ion sensor activity molecular function regulator activity metal ion sensor activity 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 regulation of postsynaptic membrane neurotransmitter receptor levels regulation of biological quality response to stimulus response to metal ion response to chemical response to calcium ion positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization membrane fusion organelle membrane fusion positive regulation of biological process regulation of vesicle fusion vesicle organization cellular component organization cellular component organization or biogenesis positive regulation of cellular process membrane organization regulation of organelle organization organelle fusion organelle organization positive regulation of transport positive regulation of vesicle fusion vesicle fusion trans-synaptic signaling synaptic signaling signaling anterograde trans-synaptic signaling cell-cell signaling chemical synaptic transmission cell communication cellular localization synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport in synapse signal release establishment of localization in cell neurotransmitter secretion neurotransmitter transport signal release from synapse 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	cell periphery cellular anatomical structure membrane plasma membrane synapse cell junction plasma membrane region synaptic membrane membrane-bounded organelle intracellular anatomical structure transport vesicle intracellular vesicle intracellular membrane-bounded organelle endomembrane system cell periphery cellular anatomical structure membrane plasma membrane synapse cell junction plasma membrane region synaptic membrane 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 presynapse endosome postsynapse transport vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR000008	C2 domain	Domain
A, B, C	IPR001565	Synaptotagmin	Domain
A, B, C	IPR035892	C2 domain superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C	OPM	Monotopic/peripheral	All beta monotopic/peripheral	C2 domain	C2 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.