1Z0K

Structure of GTP-Bound Rab4Q67L GTPase in complex with the central Rab binding domain of Rabenosyn-5

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	d1z0ka1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Rab4a	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1z0kc_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Rab4a	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1z0kb1	All alpha proteins	Long alpha-hairpin	Rabenosyn-5 Rab-binding domain-like	Rabenosyn-5 Rab-binding domain-like	FYVE finger-containing Rab5 effector protein rabenosyn-5	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1z0kd_	All alpha proteins	Long alpha-hairpin	Rabenosyn-5 Rab-binding domain-like	Rabenosyn-5 Rab-binding domain-like	automated matches	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	Ras-like P-loop GTPases	8057288	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8057288	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	e1z0kA1	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	Ras	e1z0kC1	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	Rbsn	e1z0kB1	A: alpha bundles	X: Long alpha-hairpin	H: Rabenosyn-5 Rab-binding domain-like (From Topology)	T: Rabenosyn-5 Rab-binding domain-like	F: Rbsn	ECOD (1.6)
D	Rbsn	e1z0kD1	A: alpha bundles	X: Long alpha-hairpin	H: Rabenosyn-5 Rab-binding domain-like (From Topology)	T: Rabenosyn-5 Rab-binding domain-like	F: Rbsn	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	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	4.10.860.20	Few Secondary Structures	Irregular	DNA Excision Repair, Uvrb	Chain A	CATH (4.3.0)
D	4.10.860.20	Few Secondary Structures	Irregular	DNA Excision Repair, Uvrb	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	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, D	PF11464	Rabenosyn Rab binding domain (Rbsn)	Rabenosyn Rab binding domain	Rabenosyn-5 (Rbsn) is a multivalent effector with interacts with the Rab family.Rsbn contains distinct Rab4 and Rab5 binding sites within residues 264-500 and 627-784 respectively [1]. Rab proteins are GTPases involved in the regulation of all stages ...	Rabenosyn-5 (Rbsn) is a multivalent effector with interacts with the Rab family.Rsbn contains distinct Rab4 and Rab5 binding sites within residues 264-500 and 627-784 respectively [1]. Rab proteins are GTPases involved in the regulation of all stages of membrane trafficking [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	GTP-binding protein	guanyl nucleotide binding binding nucleotide binding GDP binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding guanyl nucleotide binding binding nucleotide binding GDP binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule 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 GTP binding purine ribonucleoside triphosphate binding	localization transport cellular process establishment of localization vesicle-mediated transport vesicle-mediated transport in synapse regulation of localization import into cell regulation of biological process regulation of cellular process regulation of cellular component organization regulation of transport biological regulation regulation of vesicle-mediated transport localization transport cellular process establishment of localization vesicle-mediated transport vesicle-mediated transport in synapse regulation of localization import into cell regulation of biological process regulation of cellular process regulation of cellular component organization regulation of transport biological regulation regulation of vesicle-mediated transport cellular component organization cellular component organization or biogenesis endocytosis regulation of endocytosis antigen processing and presentation immune system process cellular response to stimulus small GTPase-mediated signal transduction response to stimulus signaling intracellular signal transduction cell communication intracellular signaling cassette Rab protein signal transduction signal transduction protein localization establishment of protein localization cellular localization nitrogen compound transport protein localization to synapse neurotransmitter receptor transport postsynaptic membrane to endosome protein localization to endosome cellular macromolecule localization neurotransmitter receptor transport protein localization to early endosome protein-containing complex localization establishment of protein localization to organelle protein transport macromolecule localization protein localization to organelle protein localization to postsynapse protein localization to cell junction receptor localization to synapse	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure vesicle membrane cytoplasmic vesicle organelle cytoplasm vesicle organelle membrane membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure vesicle membrane cytoplasmic vesicle organelle cytoplasm vesicle organelle membrane endosome membrane endosome recycling endosome endomembrane system bounding membrane of organelle recycling endosome membrane synapse postsynaptic recycling endosome postsynaptic endosome postsynapse cell junction early endosome early endosome membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle perinuclear region of cytoplasm insulin-responsive compartment secretory granule secretory vesicle glutamatergic synapse
B, D	FYVE-finger-containing Rab5 effector protein rabenosyn-5	small GTPase binding protein binding binding enzyme binding GTPase binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular localization post-Golgi vesicle-mediated transport transport intracellular transport lysosomal transport establishment of localization vesicle-mediated transport localization Golgi to vacuole transport cytosolic transport establishment of localization in cell vacuolar transport cellular process Golgi to lysosome transport cellular localization post-Golgi vesicle-mediated transport transport intracellular transport lysosomal transport establishment of localization vesicle-mediated transport localization Golgi to vacuole transport cytosolic transport establishment of localization in cell vacuolar transport cellular process Golgi to lysosome transport Golgi vesicle transport early endosome to Golgi transport endosomal transport retrograde transport, endosome to Golgi protein localization establishment of protein localization nitrogen compound transport protein transport cellular macromolecule localization macromolecule localization regulation of biological process regulation of cellular component organization regulation of cellular process biological regulation regulation of organelle organization regulation of Golgi organization cellular component organization organelle organization cellular component organization or biogenesis Golgi organization endomembrane system organization	membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle endosome membrane early endosome membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle endosome membrane early endosome membrane early endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR005225	Small GTP-binding domain	Domain
A, C	IPR001806	Small GTPase	Family
A, C	IPR041819	Rab4	Family
A, C	IPR050209	Rab GTPases family involved in membrane trafficking	Family
A, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, D	IPR036531	Rabenosyn, Rab binding domain superfamily	Homologous Superfamily
B, D	IPR013087	Zinc finger C2H2-type	Domain
B, D	IPR017455	Zinc finger, FYVE-related	Domain
B, D	IPR021565	Rabenosyn, Rab binding domain	Domain
B, D	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B, D	IPR052727	Rab4/Rab5 effector domain-containing protein	Family
B, D	IPR000306	FYVE zinc finger	Domain
B, D	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: P20338	breast carcinoma hereditary spastic paraplegia malignant mesothelioma Sjogren syndrome dermatomyositis lung adenocarcinoma pancreatic ductal adenocarcinoma gastric carcinoma lung cancer plasma cell myeloma
B, D	Pharos: Q9H1K0	atypical teratoid rhabdoid tumor large cell medulloblastoma subependymal giant cell astrocytoma glioblastoma osteosarcoma juvenile dermatomyositis 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.