4V11 | pdb_00004v11

Structure of Synaptotagmin-1 with SV2A peptide phosphorylated at Thr84

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
Pharos: Disease Associations
Membrane Protein Annotation: OPM
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8036647	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	C2_2	e4v11A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: C2 domain (From Topology)	T: C2 domain	F: C2_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	PF00168	C2 domain (C2)	C2 domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	SYNAPTIC VESICLE GLYCOPROTEIN 2A	protein binding binding kinase binding enzyme binding protein kinase binding transporter activity transmembrane transporter activity	cellular localization regulated exocytosis synaptic vesicle priming transport signaling synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport cell communication vesicle-mediated transport in synapse cellular component organization cellular component biogenesis localization synaptic signaling cellular component assembly cellular localization regulated exocytosis synaptic vesicle priming transport signaling synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport cell communication vesicle-mediated transport in synapse cellular component organization cellular component biogenesis localization synaptic signaling cellular component assembly secretion by cell signal release establishment of localization in cell protein-containing complex assembly cellular component organization or biogenesis trans-synaptic signaling regulation of biological process neurotransmitter secretion protein-containing complex organization secretion biological regulation export from cell cell-cell signaling neurotransmitter transport establishment of localization chemical synaptic transmission signal release from synapse exocytosis anterograde trans-synaptic signaling exocytic process cellular process inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis	cellular anatomical structure neuromuscular junction synapse cell junction presynapse presynaptic active zone cell-cell junction anchoring junction cell periphery plasma membrane membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle cellular anatomical structure neuromuscular junction synapse cell junction presynapse presynaptic active zone cell-cell junction anchoring junction cell periphery plasma membrane membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle transport vesicle membrane endomembrane system intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane synaptic vesicle synaptic vesicle membrane vesicle transport vesicle exocytic vesicle membrane intracellular membrane-bounded organelle cytoplasmic vesicle membrane organelle secretory vesicle cytoplasm organelle membrane exocytic vesicle GABA-ergic synapse glutamatergic synapse endoplasmic reticulum cell projection neuron projection plasma membrane bounded cell projection
A	SYNAPTOTAGMIN-1	binding calcium-dependent phospholipid binding phospholipid binding lipid 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 calcium-dependent phospholipid binding phospholipid binding lipid 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 cytosolic region 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR022308	Synaptic vesicle protein SV2	Family
B	IPR011701	Major facilitator superfamily	Family
B	IPR005828	Major facilitator, sugar transporter-like	Family
B	IPR005829	Sugar transporter, conserved site	Conserved Site
B	IPR055415	SV2A/B/C, luminal domain	Domain
B	IPR036259	MFS transporter superfamily	Homologous Superfamily
B	IPR020846	Major facilitator superfamily domain	Domain
A	IPR000008	C2 domain	Domain
A	IPR001565	Synaptotagmin	Domain
A	IPR035892	C2 domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q7L0J3	Partial Epilepsy Treatment Adjunct astrocytic tumor breast carcinoma Gaucher disease large cell medulloblastoma malignant ependymoma medulloblastoma ovarian cancer schizophrenia atypical teratoid rhabdoid tumor epilepsy glioblastoma lung cancer malignant glioma partial epilepsy Partial Epilepsy Treatment Adjunct astrocytic tumor breast carcinoma Gaucher disease large cell medulloblastoma malignant ependymoma medulloblastoma ovarian cancer schizophrenia atypical teratoid rhabdoid tumor epilepsy glioblastoma lung cancer malignant glioma partial epilepsy botulism idiopathic scoliosis lung carcinoma malignant mesothelioma non-small cell lung carcinoma
A	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

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Monotopic/peripheral	All beta monotopic/peripheral	C2 domain	C2 domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	TPO	Parent Component: THR RESID: AA0038 PSI-MOD : O-phospho-L-threonine MOD:00047

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.