6U41

1.7 angstrom structure of a pathogenic human Syt 1 C2B (D304G)

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6u41a_	All beta proteins	C2 domain-like	C2 domain (Calcium/lipid-binding domain, CaLB)	Synaptotagmin-like (S variant)	Synaptogamin I	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	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	e6u41A1	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 (utative)

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-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 phosphatidylserine binding clathrin binding cation binding ion binding calcium ion binding metal ion binding small molecule binding syntaxin-1 binding protein heterodimerization activity protein dimerization activity phosphatidylinositol-4,5-bisphosphate binding anion 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 synaptic vesicle endocytosis import into cell presynaptic endocytosis synaptic vesicle recycling endocytosis 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 detection of stimulus detection of chemical stimulus detection of calcium ion	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 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 membrane cellular anatomical entity 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 cell periphery presynapse synapse cell junction plasma membrane presynaptic membrane plasma membrane region synaptic 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 neuron to neuron synapse hippocampal mossy fiber to CA3 synapse neuron projection terminus excitatory synapse chromaffin granule membrane chromaffin granule secretory granule membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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

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.