5LOB | pdb_00005lob

Structure of the Ca2+-bound Rabphilin3A C2B- SNAP25 complex (C2 space group)

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	SNARE fusion complex	8043667	3001549	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	SNARE fusion complex	8043667	3001549	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8039052	3000965	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8039052	3000965	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8039052	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		e5lobC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Immunoglobulin-related	T: HAD-like	F:	ECOD (v294.1)
B		e5lobB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Immunoglobulin-related	T: HAD-like	F:	ECOD (v294.1)
A		e5lobA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Immunoglobulin-related	T: HAD-like	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	1.20.5.110	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
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
E, G	Synaptosomal-associated protein 25	fusogenic activity SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity monoatomic cation transmembrane transporter activity gated channel activity monoatomic ion channel activity potassium ion transmembrane transporter activity voltage-gated channel activity voltage-gated monoatomic ion channel activity potassium channel activity voltage-gated monoatomic cation channel activity monoatomic cation channel activity passive transmembrane transporter activity fusogenic activity SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity monoatomic cation transmembrane transporter activity gated channel activity monoatomic ion channel activity potassium ion transmembrane transporter activity voltage-gated channel activity voltage-gated monoatomic ion channel activity potassium channel activity voltage-gated monoatomic cation channel activity monoatomic cation channel activity passive transmembrane transporter activity voltage-gated potassium channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity protein binding binding protein domain specific binding syntaxin-1 binding SNARE binding syntaxin binding transmembrane transporter binding lipid binding cytoskeletal protein binding myosin binding calcium-dependent protein binding	positive regulation of cell communication regulation of localization regulation of cellular process regulation of hormone secretion signaling transport positive regulation of biological process positive regulation of secretion by cell hormone secretion cell communication localization positive regulation of hormone secretion regulation of secretion by cell secretion by cell positive regulation of secretion positive regulation of cell communication regulation of localization regulation of cellular process regulation of hormone secretion signaling transport positive regulation of biological process positive regulation of secretion by cell hormone secretion cell communication localization positive regulation of hormone secretion regulation of secretion by cell secretion by cell positive regulation of secretion signal release regulation of biological quality positive regulation of cellular process regulation of signaling regulation of biological process regulation of transport secretion regulation of hormone levels biological regulation export from cell cell-cell signaling establishment of localization regulation of secretion positive regulation of transport regulation of cell communication hormone transport cellular process positive regulation of signaling establishment of protein localization regulation of protein localization macromolecule localization regulation of establishment of protein localization intracellular protein localization membrane organization protein-containing complex organization membrane fusion organelle membrane fusion vesicle-mediated transport cellular component organization cellular component biogenesis vesicle organization organelle fusion organelle organization cellular component assembly protein-containing complex assembly SNARE complex assembly cellular component organization or biogenesis vesicle fusion regulation of synaptic plasticity trans-synaptic signaling modulation of chemical synaptic transmission chemical synaptic transmission positive regulation of synaptic plasticity synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization regulation of vesicle fusion regulation of vesicle-mediated transport regulation of organelle organization positive regulation of vesicle fusion multicellular organismal process axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development system development developmental process plasma membrane bounded cell projection organization nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development cellular localization establishment of localization in cell intracellular transport endosomal transport regulated exocytosis synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport in synapse calcium-ion regulated exocytosis calcium ion-regulated exocytosis of neurotransmitter neurotransmitter secretion neurotransmitter transport signal release from synapse exocytosis short-term synaptic potentiation cell junction assembly regulation of synapse structure or activity regulation of synapse assembly synapse organization regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly establishment of organelle localization dense core granule localization organelle localization presynaptic dense core vesicle exocytosis secretory granule localization vesicle localization establishment of vesicle localization neuronal dense core vesicle exocytosis dense core granule exocytosis synaptic vesicle priming exocytic process nitrogen compound transport protein localization to extracellular region peptide secretion establishment of protein localization to extracellular region protein secretion peptide transport protein transport peptide hormone secretion insulin secretion regulation of synaptic vesicle cycle behavior locomotory behavior system process learning or memory long-term memory nervous system process cognition memory learning associative learning endomembrane system organization vesicle fusion to plasma membrane synaptic vesicle fusion to presynaptic active zone membrane synaptic vesicle membrane organization positive regulation of establishment of protein localization positive regulation of insulin secretion regulation of peptide hormone secretion positive regulation of peptide hormone secretion regulation of protein secretion positive regulation of protein localization regulation of peptide secretion positive regulation of protein transport positive regulation of peptide secretion regulation of peptide transport regulation of protein transport positive regulation of protein secretion regulation of insulin secretion regulation of neuron projection development regulation of cell projection organization regulation of plasma membrane bounded cell projection organization long-term synaptic potentiation positive regulation of synaptic transmission synaptic transmission, glutamatergic regulation of glutamate secretion positive regulation of neurotransmitter secretion positive regulation of amine transport regulation of amino acid transport glutamate secretion positive regulation of neurotransmitter transport carboxylic acid transport organic acid transport acidic amino acid transport glutamate secretion, neurotransmission positive regulation of glutamate secretion, neurotransmission positive regulation of amino acid transport dicarboxylic acid transport regulation of synaptic transmission, glutamatergic L-amino acid transport L-glutamate import organic anion transport regulation of neurotransmitter transport positive regulation of glutamate secretion positive regulation of synaptic transmission, glutamatergic positive regulation of organic acid transport amino acid transport amine transport regulation of glutamate secretion, neurotransmission regulation of neurotransmitter secretion regulation of organic acid transport regulation of amine transport	cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium membrane photoreceptor inner segment intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium membrane photoreceptor inner segment intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cell periphery presynapse synapse cell junction plasma membrane presynaptic membrane plasma membrane region synaptic membrane cytoplasm glutamatergic synapse neuron projection membrane-bounded organelle Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system trans-Golgi network SNARE complex protein-containing complex synaptobrevin 2-SNAP-25-syntaxin-1a complex membrane protein complex synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex perinuclear region of cytoplasm somatodendritic compartment cell body neuronal cell body axon synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex transport vesicle intracellular vesicle cytoplasmic vesicle synaptic vesicle secretory vesicle vesicle exocytic vesicle actin-based cell projection filopodium growth cone distal axon axonal growth cone site of polarized growth cell cortex axon terminus terminal bouton neuron projection terminus ribbon synapse voltage-gated potassium channel complex plasma membrane protein complex potassium channel complex cation channel complex transporter complex transmembrane transporter complex monoatomic ion channel complex endosome extrinsic component of plasma membrane extrinsic component of synaptic membrane extrinsic component of presynaptic membrane extrinsic component of membrane BLOC complex intracellular protein-containing complex BLOC-1 complex
D, F	Synaptosomal-associated protein 25	fusogenic activity SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity monoatomic cation transmembrane transporter activity gated channel activity monoatomic ion channel activity potassium ion transmembrane transporter activity voltage-gated channel activity voltage-gated monoatomic ion channel activity potassium channel activity voltage-gated monoatomic cation channel activity monoatomic cation channel activity passive transmembrane transporter activity fusogenic activity SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity monoatomic cation transmembrane transporter activity gated channel activity monoatomic ion channel activity potassium ion transmembrane transporter activity voltage-gated channel activity voltage-gated monoatomic ion channel activity potassium channel activity voltage-gated monoatomic cation channel activity monoatomic cation channel activity passive transmembrane transporter activity voltage-gated potassium channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity protein binding binding protein domain specific binding syntaxin-1 binding SNARE binding syntaxin binding transmembrane transporter binding lipid binding cytoskeletal protein binding myosin binding calcium-dependent protein binding	positive regulation of cell communication regulation of localization regulation of cellular process regulation of hormone secretion signaling transport positive regulation of biological process positive regulation of secretion by cell hormone secretion cell communication localization positive regulation of hormone secretion regulation of secretion by cell secretion by cell positive regulation of secretion positive regulation of cell communication regulation of localization regulation of cellular process regulation of hormone secretion signaling transport positive regulation of biological process positive regulation of secretion by cell hormone secretion cell communication localization positive regulation of hormone secretion regulation of secretion by cell secretion by cell positive regulation of secretion signal release regulation of biological quality positive regulation of cellular process regulation of signaling regulation of biological process regulation of transport secretion regulation of hormone levels biological regulation export from cell cell-cell signaling establishment of localization regulation of secretion positive regulation of transport regulation of cell communication hormone transport cellular process positive regulation of signaling establishment of protein localization regulation of protein localization macromolecule localization regulation of establishment of protein localization intracellular protein localization membrane organization protein-containing complex organization membrane fusion organelle membrane fusion vesicle-mediated transport cellular component organization cellular component biogenesis vesicle organization organelle fusion organelle organization cellular component assembly protein-containing complex assembly SNARE complex assembly cellular component organization or biogenesis vesicle fusion regulation of synaptic plasticity trans-synaptic signaling modulation of chemical synaptic transmission chemical synaptic transmission positive regulation of synaptic plasticity synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization regulation of vesicle fusion regulation of vesicle-mediated transport regulation of organelle organization positive regulation of vesicle fusion multicellular organismal process axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development system development developmental process plasma membrane bounded cell projection organization nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development cellular localization establishment of localization in cell intracellular transport endosomal transport regulated exocytosis synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport in synapse calcium-ion regulated exocytosis calcium ion-regulated exocytosis of neurotransmitter neurotransmitter secretion neurotransmitter transport signal release from synapse exocytosis short-term synaptic potentiation cell junction assembly regulation of synapse structure or activity regulation of synapse assembly synapse organization regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly establishment of organelle localization dense core granule localization organelle localization presynaptic dense core vesicle exocytosis secretory granule localization vesicle localization establishment of vesicle localization neuronal dense core vesicle exocytosis dense core granule exocytosis synaptic vesicle priming exocytic process nitrogen compound transport protein localization to extracellular region peptide secretion establishment of protein localization to extracellular region protein secretion peptide transport protein transport peptide hormone secretion insulin secretion regulation of synaptic vesicle cycle behavior locomotory behavior system process learning or memory long-term memory nervous system process cognition memory learning associative learning endomembrane system organization vesicle fusion to plasma membrane synaptic vesicle fusion to presynaptic active zone membrane synaptic vesicle membrane organization positive regulation of establishment of protein localization positive regulation of insulin secretion regulation of peptide hormone secretion positive regulation of peptide hormone secretion regulation of protein secretion positive regulation of protein localization regulation of peptide secretion positive regulation of protein transport positive regulation of peptide secretion regulation of peptide transport regulation of protein transport positive regulation of protein secretion regulation of insulin secretion regulation of neuron projection development regulation of cell projection organization regulation of plasma membrane bounded cell projection organization long-term synaptic potentiation positive regulation of synaptic transmission synaptic transmission, glutamatergic regulation of glutamate secretion positive regulation of neurotransmitter secretion positive regulation of amine transport regulation of amino acid transport glutamate secretion positive regulation of neurotransmitter transport carboxylic acid transport organic acid transport acidic amino acid transport glutamate secretion, neurotransmission positive regulation of glutamate secretion, neurotransmission positive regulation of amino acid transport dicarboxylic acid transport regulation of synaptic transmission, glutamatergic L-amino acid transport L-glutamate import organic anion transport regulation of neurotransmitter transport positive regulation of glutamate secretion positive regulation of synaptic transmission, glutamatergic positive regulation of organic acid transport amino acid transport amine transport regulation of glutamate secretion, neurotransmission regulation of neurotransmitter secretion regulation of organic acid transport regulation of amine transport	cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium membrane photoreceptor inner segment intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium membrane photoreceptor inner segment intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cell periphery presynapse synapse cell junction plasma membrane presynaptic membrane plasma membrane region synaptic membrane cytoplasm glutamatergic synapse neuron projection membrane-bounded organelle Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system trans-Golgi network SNARE complex protein-containing complex synaptobrevin 2-SNAP-25-syntaxin-1a complex membrane protein complex synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex perinuclear region of cytoplasm somatodendritic compartment cell body neuronal cell body axon synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex transport vesicle intracellular vesicle cytoplasmic vesicle synaptic vesicle secretory vesicle vesicle exocytic vesicle actin-based cell projection filopodium growth cone distal axon axonal growth cone site of polarized growth cell cortex axon terminus terminal bouton neuron projection terminus ribbon synapse voltage-gated potassium channel complex plasma membrane protein complex potassium channel complex cation channel complex transporter complex transmembrane transporter complex monoatomic ion channel complex endosome extrinsic component of plasma membrane extrinsic component of synaptic membrane extrinsic component of presynaptic membrane extrinsic component of membrane BLOC complex intracellular protein-containing complex BLOC-1 complex
A, B, C	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 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
E, G	IPR000727	Target SNARE coiled-coil homology domain	Domain
E, G	IPR039077	SNAP25, N-terminal SNARE motif, chordates	Domain
E, G	IPR000928	SNAP-25 domain	Domain
D, F	IPR000727	Target SNARE coiled-coil homology domain	Domain
D, F	IPR039077	SNAP25, N-terminal SNARE motif, chordates	Domain
D, F	IPR000928	SNAP-25 domain	Domain
A, B, C	IPR017455	Zinc finger, FYVE-related	Domain
A, B, C	IPR028698	Rabphilin-3A, FYVE domain	Domain
A, B, C	IPR000008	C2 domain	Domain
A, B, C	IPR010911	Rab-binding domain	Domain
A, B, C	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B, C	IPR001565	Synaptotagmin	Domain
A, B, C	IPR043566	Rabphilin/Doc2/Noc2	Family
A, B, C	IPR047022	Rabphilin/Doc2, first C2 domain	Domain
A, B, C	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B, C	IPR035892	C2 domain superfamily	Homologous Superfamily
A, B, C	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.