2ZET

Crystal structure of the small GTPase Rab27B complexed with the Slp homology domain of Slac2-a/melanophilin

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)
A	d2zeta_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Rab27b	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth B]	d2zetb_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Rab27b	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8056340	3002022	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Ras-like P-loop GTPases	8056340	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)
A	Ras	e2zetA1	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)
C [auth B]	Ras	e2zetB1	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)
B [auth C]	FYVE_2_N	e2zetC1	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 [auth C]	FYVE_2_C	e2zetC2	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)
D	FYVE_2_N	e2zetD1	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)
D	FYVE_2_C	e2zetD2	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)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B]	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, motil ...	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
B [auth C], D	PF02318	FYVE-type zinc finger (FYVE_2)	FYVE-type zinc finger	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B]	Ras-related protein Rab-27B	protein binding binding protein domain specific binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding protein binding binding protein domain specific binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding GDP binding cytoskeletal protein binding myosin V binding myosin binding pyrophosphatase activity GTPase activity G protein activity ribonucleoside triphosphate phosphatase activity molecular function regulator activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	protein localization establishment of protein localization cellular localization nitrogen compound transport protein localization to synapse transport protein transport along microtubule microtubule-based protein transport localization cellular macromolecule localization establishment of localization in cell transport along microtubule anterograde axonal transport organic substance transport protein localization establishment of protein localization cellular localization nitrogen compound transport protein localization to synapse transport protein transport along microtubule microtubule-based protein transport localization cellular macromolecule localization establishment of localization in cell transport along microtubule anterograde axonal transport organic substance transport axo-dendritic protein transport anterograde axonal protein transport intracellular transport axonal transport establishment of localization protein localization to presynapse axo-dendritic transport protein transport macromolecule localization microtubule-based transport cellular process microtubule-based process cytoskeleton-dependent intracellular transport microtubule-based movement protein localization to cell junction intracellular protein transport synaptic vesicle endocytosis import into cell synaptic vesicle cycle vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling endocytosis regulation of localization regulation of cellular process positive regulation of biological process positive regulation of secretion by cell positive regulation of exocytosis regulation of secretion by cell secretion by cell positive regulation of secretion positive regulation of cellular process regulation of biological process regulation of transport secretion biological regulation export from cell regulation of vesicle-mediated transport regulation of secretion positive regulation of transport exocytosis regulation of exocytosis multivesicular body sorting pathway	membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle Golgi stack cytoplasm pigment granule intracellular vesicle membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle Golgi stack cytoplasm pigment granule intracellular vesicle melanosome cytoplasmic vesicle vesicle endosome membrane endosome membrane multivesicular body membrane late endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane late endosome organelle membrane multivesicular body cell periphery apical part of cell plasma membrane plasma membrane region apical plasma membrane transport vesicle secretory vesicle exocytic vesicle secretory granule trans-Golgi network transport vesicle clathrin-coated vesicle coated vesicle Golgi-associated vesicle zymogen granule zymogen granule membrane secretory granule membrane synapse transport vesicle membrane presynapse synaptic vesicle synaptic vesicle membrane cell junction exocytic vesicle membrane neuron projection cytoplasm axon axon cytoplasm neuron projection cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection cell projection
B [auth C], D	Melanophilin	small GTPase binding protein binding binding enzyme binding GTPase binding protein-macromolecule adaptor activity molecular adaptor activity cytoskeletal protein binding actin binding myosin binding myosin V binding microtubule plus-end binding microtubule binding tubulin binding small GTPase binding protein binding binding enzyme binding GTPase binding protein-macromolecule adaptor activity molecular adaptor activity cytoskeletal protein binding actin binding myosin binding myosin V binding microtubule plus-end binding microtubule binding tubulin binding cation binding ion binding metal ion binding small molecule binding	developmental process pigment cell differentiation pigmentation cellular developmental process cell differentiation developmental pigmentation melanocyte differentiation cellular process protein localization cellular localization establishment of protein localization nitrogen compound transport transport organic substance transport developmental process pigment cell differentiation pigmentation cellular developmental process cell differentiation developmental pigmentation melanocyte differentiation cellular process protein localization cellular localization establishment of protein localization nitrogen compound transport transport organic substance transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization intracellular protein transport vesicle localization pigment granule localization organelle localization cellular pigmentation melanosome localization protein targeting	membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle cytoskeleton intracellular non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle cytoskeleton intracellular non-membrane-bounded organelle actin cytoskeleton non-membrane-bounded organelle somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection protein-containing complex myosin complex unconventional myosin complex cell cortex cortical cytoskeleton cell periphery cortical actin cytoskeleton actin filament bundle actomyosin stress fiber contractile actin filament bundle microtubule organizing center microtubule cytoskeleton perinuclear region of cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B]	IPR041837	Rab27a/b	Family
A, C [auth B]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C [auth B]	IPR001806	Small GTPase	Family
A, C [auth B]	IPR005225	Small GTP-binding protein domain	Domain
B [auth C], D	IPR006788	Rab effector MyRIP/Melanophilin	Domain
B [auth C], D	IPR010911	Rab-binding domain	Domain
B [auth C], D	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
B [auth C], D	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B [auth C], D	IPR041282	FYVE-type zinc finger	Domain
B [auth C], D	IPR037442	Melanophilin, FYVE-related domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.