1ZBD | pdb_00001zbd

STRUCTURAL BASIS OF RAB EFFECTOR SPECIFICITY: CRYSTAL STRUCTURE OF THE SMALL G PROTEIN RAB3A COMPLEXED WITH THE EFFECTOR DOMAIN OF RABPHILIN-3A

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
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)
B	d1zbdb_	Small proteins	FYVE/PHD zinc finger	FYVE/PHD zinc finger	FYVE, a phosphatidylinositol-3-phosphate binding domain	Effector domain of rabphilin-3a	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1zbda_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Rab3a	Norway 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	SCOP2 Family	FYVE, a phosphatidylinositol-3-phosphate binding domain	8026957	4003768	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	FYVE/PHD zinc finger	8039336	3001459	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8057402	3002022	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)
B	FYVE_2_N	e1zbdB2	A: alpha bundles	X: Long alpha-hairpin	H: Slp2a Rab-binding domain-like (From Topology)	T: Slp2a Rab-binding domain-like	F: FYVE_2_N	ECOD (1.6)
B	FYVE_2_C	e1zbdB3	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: FYVE_2_C	ECOD (1.6)
A	Ras	e1zbdA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF02318	FYVE-type zinc finger (FYVE_2)	FYVE-type zinc finger	-	Family
A	PF00071	Ras family (Ras)	Ras family	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motili ...	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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 nitrogen compound transport 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
A	RABPHILIN-3A	ATPase activator activity molecular function activator activity molecular function regulator activity ATPase regulator activity protein-macromolecule adaptor activity molecular adaptor activity ATPase binding protein binding binding enzyme binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides ATPase activator activity molecular function activator activity molecular function regulator activity ATPase regulator activity protein-macromolecule adaptor activity molecular adaptor activity ATPase binding protein binding binding enzyme binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity GDP-dissociation inhibitor binding GTP-dependent protein binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cytoskeletal protein binding myosin V binding myosin binding	regulated exocytosis transport secretion export from cell establishment of localization vesicle-mediated transport localization secretion by cell exocytosis cellular process calcium-ion regulated exocytosis vesicle localization establishment of organelle localization cellular localization regulated exocytosis transport secretion export from cell establishment of localization vesicle-mediated transport localization secretion by cell exocytosis cellular process calcium-ion regulated exocytosis vesicle localization establishment of organelle localization cellular localization establishment of vesicle localization organelle localization establishment of localization in cell synaptic vesicle localization synaptic vesicle transport cellular response to stimulus regulation of biological process small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication intracellular signaling cassette Rab protein signal transduction signal transduction synaptic signaling signal release evoked neurotransmitter secretion trans-synaptic signaling neurotransmitter secretion cell-cell signaling neurotransmitter transport chemical synaptic transmission signal release from synapse anterograde trans-synaptic signaling neuromuscular synaptic transmission multicellular organismal process axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development cellular component organization or biogenesis 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 response to electrical stimulus response to abiotic stimulus regulation of localization membrane fusion synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport in synapse vesicle organization regulation of synaptic vesicle membrane organization endomembrane system organization vesicle fusion to plasma membrane regulation of organelle organization organelle fusion vesicle fusion regulation of cellular component organization organelle membrane fusion regulation of vesicle fusion regulation of synaptic vesicle fusion to presynaptic active zone membrane membrane organization regulation of transport synaptic vesicle fusion to presynaptic active zone membrane regulation of vesicle-mediated transport organelle organization synaptic vesicle membrane organization exocytic process sexual reproduction reproductive process fertilization acrosome reaction acrosomal vesicle exocytosis single fertilization synaptic vesicle priming regulation of synaptic vesicle priming cellular component biogenesis regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly protein-containing complex organization regulation of cellular component biogenesis maintenance of synapse structure cell junction maintenance maintenance of presynaptic active zone structure cell junction organization cellular component maintenance presynaptic active zone organization synapse organization modulation of chemical synaptic transmission regulation of regulated secretory pathway regulation of secretion by cell regulation of signaling regulation of neurotransmitter transport regulation of synaptic vesicle exocytosis regulation of secretion regulation of trans-synaptic signaling regulation of neurotransmitter secretion regulation of exocytosis regulation of cell communication establishment of protein localization nitrogen compound transport hormone secretion protein localization to extracellular region peptide secretion amide transport regulation of biological quality intracellular protein localization regulation of hormone levels establishment of protein localization to extracellular region protein secretion peptide transport protein transport peptide hormone secretion macromolecule localization hormone transport insulin secretion 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 transport synaptic vesicle recycling lysosome localization vacuolar localization monoamine transport regulation of catecholamine secretion organic hydroxy compound transport dopamine transport catecholamine transport dopamine secretion catecholamine secretion amine transport regulation of amine transport regulation of dopamine secretion tube development animal organ development respiratory tube development lung development respiratory system development wound healing plasma membrane repair regulation of plasma membrane organization response to stress plasma membrane organization regulation of plasma membrane repair response to wounding regulation of neuronal synaptic plasticity regulation of synaptic plasticity regulation of short-term neuronal synaptic plasticity synaptic vesicle clustering system process sensory perception nervous system process sensory perception of touch sensory perception of mechanical stimulus respiratory system process respiratory gaseous exchange by respiratory system secretory granule localization calcium ion-regulated exocytosis of neurotransmitter dense core granule exocytosis presynaptic modulation of chemical synaptic transmission regulation of presynaptic dense core granule exocytosis regulation of dense core granule exocytosis regulation of calcium ion-dependent exocytosis of neurotransmitter regulation of calcium ion-dependent exocytosis dense core granule localization presynaptic dense core vesicle exocytosis neuronal dense core vesicle exocytosis mitochondrion organization post-embryonic development synaptic vesicle maturation developmental maturation	presynapse cellular anatomical structure synapse cell junction presynaptic active zone intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle presynapse cellular anatomical structure synapse cell junction presynaptic active zone intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle secretory granule secretory vesicle vesicle perinuclear region of cytoplasm transport vesicle membrane bounding membrane of organelle vesicle membrane synaptic vesicle synaptic vesicle membrane transport vesicle membrane exocytic vesicle membrane cytoplasmic vesicle membrane organelle membrane exocytic vesicle axon cell projection neuron projection plasma membrane bounded cell projection postsynapse acrosomal vesicle axon terminus distal axon terminal bouton neuron projection terminus cell periphery plasma membrane lytic vacuole vacuole lysosome protein-containing complex endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR017455	Zinc finger, FYVE-related	Domain
B	IPR028698	Rabphilin-3A, FYVE domain	Domain
B	IPR000008	C2 domain	Domain
B	IPR010911	Rab-binding domain	Domain
B	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
B	IPR001565	Synaptotagmin	Domain
B	IPR043566	Rabphilin/Doc2/Noc2	Family
B	IPR047022	Rabphilin/Doc2, first C2 domain	Domain
B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B	IPR035892	C2 domain superfamily	Homologous Superfamily
B	IPR041282	FYVE-type zinc finger	Domain
A	IPR037872	Rab3	Family
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR050305	Small GTPase superfamily, Rab	Family
A	IPR005225	Small GTP-binding domain	Domain
A	IPR001806	Small GTPase	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Monotopic/peripheral	All beta monotopic/peripheral	FYVE/PHD zinc finger	FYVE, a phosphatidylinositol-3-phosphate binding 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.