2D8K | pdb_00002d8k

Solution structure of the first C2 domain of synaptotagmin VII

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2d8ka1	All beta proteins	C2 domain-like	C2 domain (Calcium/lipid-binding domain, CaLB)	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2d8ka3	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2d8ka2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Synaptotagmin-like (S variant)	8072586	4002234	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8072587	3000965	SCOP2 (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	e2d8kA1	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
A	synaptotagmin VII	clathrin binding protein binding binding cation binding ion binding calcium ion binding metal ion binding small molecule binding SNARE binding syntaxin binding phosphatidylinositol-4,5-bisphosphate binding anion binding phosphatidylinositol bisphosphate binding phospholipid binding clathrin binding protein binding binding cation binding ion binding calcium ion binding metal ion binding small molecule binding SNARE binding syntaxin binding phosphatidylinositol-4,5-bisphosphate binding anion binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding calcium-dependent phospholipid binding molecular sensor activity calcium ion sensor activity molecular function regulator activity metal ion sensor activity calmodulin binding	import into cell transport membrane fusion organelle membrane fusion vesicle-mediated transport vesicle organization cellular component organization cellular component biogenesis localization lysosome organization cellular component assembly phagolysosome assembly phagocytosis cellular component organization or biogenesis import into cell transport membrane fusion organelle membrane fusion vesicle-mediated transport vesicle organization cellular component organization cellular component biogenesis localization lysosome organization cellular component assembly phagolysosome assembly phagocytosis cellular component organization or biogenesis membrane organization vacuole organization organelle assembly lytic vacuole organization phagosome-lysosome fusion phagosome maturation establishment of localization organelle fusion organelle organization cellular process endocytosis vesicle fusion regulation of localization regulated exocytosis regulation of biological process regulation of cellular process regulation of calcium ion-dependent exocytosis secretion regulation of transport biological regulation export from cell regulation of vesicle-mediated transport regulation of secretion regulation of regulated secretory pathway secretion by cell regulation of secretion by cell exocytosis regulation of exocytosis calcium-ion regulated exocytosis synaptic vesicle recycling cellular localization establishment of localization in cell synaptic vesicle cycle vesicle-mediated transport in synapse regulation of cellular component organization regulation of synaptic vesicle recycling presynaptic endocytosis regulation of synaptic vesicle endocytosis regulation of endocytosis synaptic vesicle endocytosis regulation of phagocytosis establishment of protein localization nitrogen compound transport regulation of hormone secretion regulation of protein localization regulation of peptide secretion signaling hormone secretion protein localization to extracellular region cell communication peptide secretion amide transport signal release intracellular protein localization regulation of biological quality regulation of peptide hormone secretion regulation of signaling regulation of hormone levels regulation of peptide transport regulation of establishment of protein localization establishment of protein localization to extracellular region cell-cell signaling regulation of protein transport protein secretion regulation of protein secretion peptide transport protein transport regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport regulation of cell communication insulin secretion calcium ion regulated lysosome exocytosis synaptic vesicle exocytosis synaptic signaling calcium ion-regulated exocytosis of neurotransmitter trans-synaptic signaling neurotransmitter secretion neurotransmitter transport chemical synaptic transmission signal release from synapse anterograde trans-synaptic signaling positive regulation of biological process positive regulation of secretion by cell positive regulation of exocytosis positive regulation of secretion positive regulation of regulated secretory pathway positive regulation of cellular process positive regulation of calcium ion-dependent exocytosis positive regulation of transport positive regulation of organelle 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 positive regulation of vesicle fusion positive regulation of cellular component organization calcium-dependent activation of synaptic vesicle fusion regulation of 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 regulation of synaptic plasticity modulation of chemical synaptic transmission short-term synaptic potentiation regulation of trans-synaptic signaling intracellular lipid transport intracellular cholesterol transport vesicle-mediated cholesterol transport lipid localization intracellular transport lipid transport organic hydroxy compound transport intracellular sterol transport cytosolic transport cholesterol transport sterol transport wound healing response to stimulus plasma membrane repair response to stress plasma membrane organization response to wounding multicellular organismal process tissue remodeling regulation of bone remodeling bone remodeling regulation of multicellular organismal process regulation of tissue remodeling glucagon secretion regulation of glucagon secretion	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane presynapse synapse cell junction presynaptic membrane plasma membrane region synaptic membrane dense core granule intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle secretory granule secretory vesicle early phagosome phagocytic vesicle endocytic vesicle lytic vacuole vacuole lysosome neuron to neuron synapse hippocampal mossy fiber to CA3 synapse phagocytic vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane endocytic vesicle membrane organelle membrane vacuolar membrane lytic vacuole membrane lysosomal membrane peroxisome microbody microbody membrane peroxisomal membrane transport vesicle membrane synaptic vesicle synaptic vesicle membrane transport vesicle exocytic vesicle membrane exocytic vesicle axon cell projection neuron projection plasma membrane bounded cell projection

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000008	C2 domain	Domain
A	IPR001565	Synaptotagmin	Domain
A	IPR037732	Synaptotagmin 7, C2A domain	Domain
A	IPR037741	Synaptotagmin 7, C2B domain	Domain
A	IPR035892	C2 domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O43581	astrocytic tumor heart disease lung carcinoma medulloblastoma ovarian cancer primitive neuroectodermal tumor atypical teratoid rhabdoid tumor hypertensive disorder malignant ependymoma oligodendroglioma pilocytic astrocytoma glioblastoma large cell medulloblastoma malignant glioma osteosarcoma astrocytic tumor heart disease lung carcinoma medulloblastoma ovarian cancer primitive neuroectodermal tumor atypical teratoid rhabdoid tumor hypertensive disorder malignant ependymoma oligodendroglioma pilocytic astrocytoma glioblastoma large cell medulloblastoma malignant glioma osteosarcoma pituitary cancer

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A	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.