2CM6 | pdb_00002cm6

crystal structure of the C2B domain of rabphilin3A

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2cm6b_	All beta proteins	C2 domain-like	C2 domain (Calcium/lipid-binding domain, CaLB)	Synaptotagmin-like (S variant)	automated matches	RAT (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d2cm6a_	All beta proteins	C2 domain-like	C2 domain (Calcium/lipid-binding domain, CaLB)	Synaptotagmin-like (S variant)	automated matches	RAT (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8039052	3000965	SCOP2B (2022-06-29)
A	SCOP2 Family	Synaptotagmin-like (S variant)	8026673	4002234	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8039052	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)
B	Alpha-L-AF_C	e2cm6B1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Alpha-L-AF_C	ECOD (v294.1)
A	Alpha-L-AF_C	e2cm6A1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Alpha-L-AF_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	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	RABPHILIN-3A	small GTPase binding protein binding binding enzyme binding GTPase binding cation binding ion binding calcium ion binding metal ion binding small molecule binding phospholipid binding lipid binding phosphatidylinositol-4,5-bisphosphate binding anion binding small GTPase binding protein binding binding enzyme binding GTPase binding cation binding ion binding calcium ion binding metal ion binding small molecule binding phospholipid binding lipid binding phosphatidylinositol-4,5-bisphosphate binding anion binding phosphatidylinositol bisphosphate binding phosphatidylinositol phosphate binding phosphatidylinositol binding calcium-dependent phospholipid binding phosphate ion binding protein-containing complex binding transition metal ion binding zinc ion binding alcohol binding inositol 1,4,5 trisphosphate binding selenium binding	cellular response to stimulus regulation of localization regulation of cellular process response to stimulus signaling transport regulation of signaling receptor activity regulation of transmembrane transporter activity regulation of signal transduction cell communication localization signal transduction regulation of NMDA receptor activity regulation of biological process cellular response to stimulus regulation of localization regulation of cellular process response to stimulus signaling transport regulation of signaling receptor activity regulation of transmembrane transporter activity regulation of signal transduction cell communication localization signal transduction regulation of NMDA receptor activity regulation of biological process regulation of signaling regulation of transport biological regulation establishment of localization transmembrane transport regulation of molecular function regulation of transmembrane transport regulation of response to stimulus regulation of neurotransmitter receptor activity regulation of cell communication cellular process cellular localization synaptic signaling secretion by cell signal release establishment of localization in cell spontaneous synaptic transmission trans-synaptic signaling neurotransmitter secretion secretion cell-cell signaling export from cell neurotransmitter transport spontaneous neurotransmitter secretion chemical synaptic transmission signal release from synapse anterograde trans-synaptic signaling establishment of protein localization intracellular transport protein transport macromolecule localization intracellular protein localization intracellular protein transport cellular component organization cell junction organization dendritic spine organization postsynapse organization plasma membrane bounded cell projection organization cell projection organization neuron projection organization synapse organization cellular component organization or biogenesis regulated exocytosis regulation of calcium ion-dependent exocytosis positive regulation of biological process positive regulation of secretion by cell vesicle-mediated transport positive regulation of exocytosis regulation of regulated secretory pathway regulation of secretion by cell positive regulation of secretion positive regulation of regulated secretory pathway positive regulation of cellular process calcium-ion regulated exocytosis positive regulation of calcium ion-dependent exocytosis regulation of vesicle-mediated transport regulation of secretion exocytosis positive regulation of transport regulation of exocytosis positive regulation of organelle organization membrane fusion synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport in synapse 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 synaptic vesicle priming cellular component biogenesis cellular component assembly protein-containing complex assembly protein-containing complex organization	cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle extrinsic component of synaptic vesicle membrane transport vesicle membrane extrinsic component of organelle membrane presynapse bounding membrane of organelle vesicle membrane synaptic vesicle synaptic vesicle membrane transport vesicle exocytic vesicle membrane cytoplasmic vesicle membrane organelle membrane extrinsic component of membrane exocytic vesicle cholinergic synapse protein-containing complex cell projection neuron projection plasma membrane bounded cell projection neuromuscular junction neuron spine dendritic spine somatodendritic compartment dendrite dendritic tree

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR017455	Zinc finger, FYVE-related	Domain
A, B	IPR028698	Rabphilin-3A, FYVE domain	Domain
A, B	IPR000008	C2 domain	Domain
A, B	IPR010911	Rab-binding domain	Domain
A, B	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B	IPR001565	Synaptotagmin	Domain
A, B	IPR043566	Rabphilin/Doc2/Noc2	Family
A, B	IPR047022	Rabphilin/Doc2, first C2 domain	Domain
A, B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B	IPR035892	C2 domain superfamily	Homologous Superfamily
A, B	IPR041282	FYVE-type zinc finger	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.