3QBT

Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp

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	d3qbta_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth C]	d3qbtc_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth E]	d3qbte_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth G]	d3qbtg_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	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	8089844	3002022	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Ras-like P-loop GTPases	8089844	3002022	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	Ras-like P-loop GTPases	8089844	3002022	SCOP2B (2022-06-29)
D [auth G]	SCOP2B Superfamily	Ras-like P-loop GTPases	8089844	3002022	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	PapD-like	8053471	3002067	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	PapD-like	8053471	3002067	SCOP2B (2022-06-29)
G [auth F]	SCOP2B Superfamily	PapD-like	8053471	3002067	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	PapD-like	8053471	3002067	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	e3qbtA1	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]	Ras	e3qbtC1	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 E]	Ras	e3qbtE1	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)
D [auth G]	Ras	e3qbtG1	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)
E [auth B]	ASH	e3qbtB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: ASH	ECOD (1.6)
F [auth D]	ASH	e3qbtD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: ASH	ECOD (1.6)
G [auth F]	ASH	e3qbtF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: ASH	ECOD (1.6)
H	ASH	e3qbtH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: ASH	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)
B [auth C]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C [auth E]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D [auth G]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E [auth B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], C [auth E], D [auth G]	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
E [auth B], F [auth D], G [auth F], H	PF21310	Inositol polyphosphate 5-phosphatase OCRL-like, ASH domain (OCRL-like_ASH)	Inositol polyphosphate 5-phosphatase OCRL-like, ASH domain	This domain is found in Inositol polyphosphate 5-phosphatase OCRL from humans and similar eukaryotic proteins. OCRL is an enzyme that dephosphorylate the 5' position of the inositol ring. It is thought to help coordinate intracellular membrane traffi ...	This domain is found in Inositol polyphosphate 5-phosphatase OCRL from humans and similar eukaryotic proteins. OCRL is an enzyme that dephosphorylate the 5' position of the inositol ring. It is thought to help coordinate intracellular membrane traffic through changes in the phosphoinositide composition of associated membranes. Mutations in this protein are responsible for Lowe syndrome. This entry represents a domain found C-terminal to Pfam:PF03372 and N-terminal to Pfam:PF00620. It is comprised by two layers of beta- sheets and is closely related to the members of the family of immunoglobulin-like beta-sandwiches [1,3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C], C [auth E], D [auth G]	Ras-related protein Rab-8A	small GTPase binding protein binding binding enzyme binding GTPase binding protein tyrosine kinase binding kinase binding protein kinase 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 small GTPase binding protein binding binding enzyme binding GTPase binding protein tyrosine kinase binding kinase binding protein kinase 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 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	protein localization cellular localization establishment of protein localization nitrogen compound transport protein localization to synapse transport neurotransmitter receptor transport to postsynaptic membrane establishment of protein localization to postsynaptic membrane vesicle-mediated transport neurotransmitter receptor transport to plasma membrane localization cellular macromolecule localization regulation of biological quality protein localization to cell periphery protein localization cellular localization establishment of protein localization nitrogen compound transport protein localization to synapse transport neurotransmitter receptor transport to postsynaptic membrane establishment of protein localization to postsynaptic membrane vesicle-mediated transport neurotransmitter receptor transport to plasma membrane localization cellular macromolecule localization regulation of biological quality protein localization to cell periphery protein localization to postsynaptic membrane neurotransmitter receptor transport establishment of protein localization to membrane biological regulation localization within membrane protein localization to membrane establishment of localization protein-containing complex localization vesicle-mediated transport to the plasma membrane regulation of postsynaptic membrane neurotransmitter receptor levels protein transport macromolecule localization cellular process protein localization to postsynapse protein localization to cell junction receptor localization to synapse cellular catabolic process catabolic process cellular metabolic process autophagy metabolic process process utilizing autophagic mechanism protein localization to plasma membrane 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 regulation of localization regulation of biological process regulation of cellular process regulation of protein localization regulation of transport regulation of establishment of protein localization regulation of protein transport regulation of cellular localization regulation of neuronal synaptic plasticity regulation of synaptic plasticity trans-synaptic signaling regulation of signaling regulation of long-term neuronal synaptic plasticity modulation of chemical synaptic transmission signaling cell-cell signaling chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication vesicle-mediated transport in synapse secretion establishment of protein localization to extracellular region export from cell protein secretion protein localization to extracellular region secretion by cell protein localization to cilium protein localization to organelle membrane docking organelle localization by membrane tethering exocytosis organelle localization vesicle docking exocytic process vesicle docking involved in exocytosis membrane organization membrane fusion organelle membrane fusion vesicle organization organelle fusion organelle organization Golgi vesicle fusion to target membrane vesicle fusion Golgi vesicle transport organelle assembly plasma membrane bounded cell projection assembly cellular component biogenesis cellular component assembly cilium assembly cilium organization cell projection assembly cellular response to nitrogen compound cellular response to stimulus response to stimulus response to endogenous stimulus response to peptide hormone response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical response to insulin cellular response to insulin stimulus cellular response to hormone stimulus regulation of cellular metabolic process regulation of catabolic process regulation of autophagy regulation of cellular catabolic process regulation of metabolic process intracellular transport endocytic recycling endosomal transport establishment of localization in cell establishment of protein localization to plasma membrane neurotransmitter receptor transport, endosome to plasma membrane neurotransmitter receptor transport, endosome to postsynaptic membrane endosome to plasma membrane protein transport intracellular protein transport Golgi organization endomembrane system organization	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol synapse extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol synapse cell junction glutamatergic synapse membrane intracellular vesicle phagocytic vesicle intracellular membrane-bounded organelle intracellular organelle phagocytic vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane organelle membrane endocytic vesicle Golgi membrane Golgi apparatus endomembrane system neuron spine neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection postsynapse dendrite dendritic tree endosome membrane endosome cell body neuronal cell body transport vesicle presynapse synaptic vesicle secretory vesicle exocytic vesicle cilium ciliary basal body microtubule organizing center cytoskeleton intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle midbody centrosome centriole cell periphery plasma membrane non-motile cilium ciliary membrane plasma membrane region cell projection membrane trans-Golgi network transport vesicle clathrin-coated vesicle coated vesicle Golgi-associated vesicle recycling endosome recycling endosome membrane postsynaptic density neuron to neuron synapse postsynaptic specialization asymmetric synapse Golgi apparatus subcompartment organelle subcompartment trans-Golgi network membrane trans-Golgi network ciliary base
E [auth B], F [auth D], G [auth F], H	Inositol polyphosphate 5-phosphatase OCRL-1	small GTPase binding protein binding binding enzyme binding GTPase binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity phosphatidylinositol phosphate phosphatase activity catalytic activity phosphatidylinositol phosphate 4-phosphatase activity inositol trisphosphate phosphatase activity inositol-polyphosphate 5-phosphatase activity small GTPase binding protein binding binding enzyme binding GTPase binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity phosphatidylinositol phosphate phosphatase activity catalytic activity phosphatidylinositol phosphate 4-phosphatase activity inositol trisphosphate phosphatase activity inositol-polyphosphate 5-phosphatase activity inositol phosphate phosphatase activity GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity inositol-1,4,5-trisphosphate 5-phosphatase activity phosphatidylinositol trisphosphate phosphatase activity phosphatidylinositol phosphate 5-phosphatase activity phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity phosphatidylinositol bisphosphate phosphatase activity phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity phosphatidylinositol-3,5-bisphosphate phosphatase activity phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity phosphatidylinositol-4,5-bisphosphate phosphatase activity inositol tetrakisphosphate phosphatase activity inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity	phosphatidylinositol metabolic process dephosphorylation cellular metabolic process glycerophospholipid metabolic process lipid modification primary metabolic process phospholipid metabolic process organophosphate metabolic process phosphatidylinositol dephosphorylation phospholipid dephosphorylation phosphate-containing compound metabolic process cellular lipid metabolic process metabolic process cellular process phosphatidylinositol metabolic process dephosphorylation cellular metabolic process glycerophospholipid metabolic process lipid modification primary metabolic process phospholipid metabolic process organophosphate metabolic process phosphatidylinositol dephosphorylation phospholipid dephosphorylation phosphate-containing compound metabolic process cellular lipid metabolic process metabolic process cellular process glycerolipid metabolic process phosphorus metabolic process lipid metabolic process polyol metabolic process organic hydroxy compound metabolic process alcohol metabolic process inositol phosphate metabolic process small molecule metabolic process cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation signal transduction cell communication organelle assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization organelle organization cellular component assembly cilium assembly cellular component organization or biogenesis cilium organization cell projection assembly developmental process multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development glycerophospholipid biosynthetic process cellular biosynthetic process lipid biosynthetic process phospholipid biosynthetic process phosphatidylinositol biosynthetic process biosynthetic process glycerolipid biosynthetic process organophosphate biosynthetic process membrane organization	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 clathrin-coated pit membrane 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 clathrin-coated pit membrane intracellular vesicle cytoplasmic vesicle clathrin-coated vesicle coated vesicle vesicle Golgi-associated vesicle cytosol cell periphery plasma membrane lytic vacuole vacuole lysosome non-motile cilium 9+0 non-motile cilium cilium neuron projection photoreceptor outer segment plasma membrane bounded cell projection cell projection photoreceptor cell cilium early endosome endosome phagocytic vesicle phagocytic vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane endocytic vesicle membrane organelle membrane endocytic vesicle trans-Golgi network endosome membrane early endosome membrane nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth E], D [auth G]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B [auth C], C [auth E], D [auth G]	IPR050305	Small GTPase superfamily, Rab	Family
A, B [auth C], C [auth E], D [auth G]	IPR005225	Small GTP-binding domain	Domain
A, B [auth C], C [auth E], D [auth G]	IPR001806	Small GTPase	Family
E [auth B], F [auth D], G [auth F], H	IPR037793	OCRL1/INPP5B, INPP5c domain	Domain
E [auth B], F [auth D], G [auth F], H	IPR037787	OCRL1, PH domain	Domain
E [auth B], F [auth D], G [auth F], H	IPR031995	Inositol polyphosphate 5-phosphatase, clathrin binding domain	Domain
E [auth B], F [auth D], G [auth F], H	IPR048869	OCRL-1/2, ASH domain	Domain
E [auth B], F [auth D], G [auth F], H	IPR008936	Rho GTPase activation protein	Homologous Superfamily
E [auth B], F [auth D], G [auth F], H	IPR000198	Rho GTPase-activating protein domain	Domain
E [auth B], F [auth D], G [auth F], H	IPR000300	Inositol polyphosphate-related phosphatase	Domain
E [auth B], F [auth D], G [auth F], H	IPR047078	Inositol polyphosphate 5-phosphatase OCRL, RhoGAP	Domain
E [auth B], F [auth D], G [auth F], H	IPR046985	Inositol 5-phosphatase	Family
E [auth B], F [auth D], G [auth F], H	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
E [auth B], F [auth D], G [auth F], H	IPR036691	Endonuclease/exonuclease/phosphatase superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B [auth C], C [auth E], D [auth G]	Pharos: P61006	rheumatoid arthritis astrocytic tumor plasma cell myeloma cancer psoriasis ovarian cancer
E [auth B], F [auth D], G [auth F], H	Pharos: Q01968	oculocerebrorenal syndrome Dent disease type 2 Dent disease cataract Dent disease type 1 leukodystrophy congenital anomaly of kidney and urinary tract lung cancer osteosarcoma intellectual disability lung carcinoma Phosphatidylinositol 4,5-Bisphosphate 5-Phosphatase Deficiency

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.