4LHY

Crystal structure of GDP-bound Rab8:Rabin8

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)
B	d4lhyb_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Rab8a	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4lhya_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Rab8a	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)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8089844	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8089844	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	Ras	e4lhyB1	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)
A	Ras	e4lhyA1	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	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	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)
C	1.20.5.4880	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
D	1.20.5.4880	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
E	1.20.5.4880	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
F	1.20.5.4880	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, 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
C, D, E, F	PF06428	GDP/GTP exchange factor Sec2p (Sec2p)	GDP/GTP exchange factor Sec2p	-	Coiled-coil

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	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 catabolic 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 catabolic process regulation of autophagy 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 cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol synapse extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space 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 intracellular membraneless organelle cilium ciliary basal body microtubule organizing center cytoskeleton membraneless organelle microtubule cytoskeleton midbody centrosome centriole cell periphery plasma membrane non-motile cilium lytic vacuole vacuole lysosome 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 Golgi apparatus subcompartment organelle subcompartment trans-Golgi network membrane trans-Golgi network ciliary base
C, D, E, F	Rab-3A-interacting protein	GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity protein binding binding enzyme binding GTPase binding identical protein binding	filopodium assembly regulation of cellular component organization regulation of cellular process cell projection organization negative regulation of filopodium assembly negative regulation of biological process regulation of filopodium assembly plasma membrane bounded cell projection assembly cellular component organization cellular component biogenesis negative regulation of plasma membrane bounded cell projection assembly cellular component assembly negative regulation of cellular process cellular component organization or biogenesis filopodium assembly regulation of cellular component organization regulation of cellular process cell projection organization negative regulation of filopodium assembly negative regulation of biological process regulation of filopodium assembly plasma membrane bounded cell projection assembly cellular component organization cellular component biogenesis negative regulation of plasma membrane bounded cell projection assembly cellular component assembly negative regulation of cellular process cellular component organization or biogenesis negative regulation of cell projection organization regulation of biological process plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization regulation of cell projection assembly biological regulation regulation of cellular component biogenesis regulation of plasma membrane bounded cell projection assembly cellular process cell projection assembly regulation of plasma membrane bounded cell projection organization Golgi to plasma membrane transport cellular localization post-Golgi vesicle-mediated transport transport localization within membrane establishment of localization vesicle-mediated transport vesicle-mediated transport to the plasma membrane localization Golgi vesicle transport ciliary basal body-plasma membrane docking organelle assembly membrane docking organelle localization by membrane tethering organelle organization organelle localization cilium assembly cilium organization protein localization establishment of protein localization nitrogen compound transport protein transport cellular macromolecule localization macromolecule localization positive regulation of organelle organization positive regulation of cellular component organization positive regulation of biological process positive regulation of cell projection organization positive regulation of cellular process positive regulation of cellular component biogenesis regulation of organelle organization positive regulation of cilium assembly regulation of cilium assembly regulation of organelle assembly positive regulation of plasma membrane bounded cell projection assembly positive regulation of organelle assembly protein localization to organelle secretion by cell exocytosis secretion export from cell protein localization to cilium protein localization to motile cilium establishment of protein localization to membrane protein targeting protein localization to membrane protein targeting to membrane	membrane-bounded organelle intracellular anatomical structure transport vesicle intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle Golgi to plasma membrane transport vesicle organelle secretory vesicle cytoplasm vesicle membrane-bounded organelle intracellular anatomical structure transport vesicle intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle Golgi to plasma membrane transport vesicle organelle secretory vesicle cytoplasm vesicle exocytic vesicle cell projection cell leading edge plasma membrane bounded cell projection lamellipodium somatodendritic compartment proximal dendrite dendrite dendritic tree neuron projection centrosome microtubule organizing center cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytosol Golgi apparatus subcompartment Golgi apparatus organelle subcompartment membrane trans-Golgi network membrane trans-Golgi network organelle membrane perinuclear region of cytoplasm cilium ciliary basal body nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR050305	Small GTPase superfamily, Rab	Family
A, B	IPR005225	Small GTP-binding domain	Domain
A, B	IPR001806	Small GTPase	Family
C, D, E, F	IPR009449	GDP/GTP exchange factor Sec2, N-terminal	Domain
C, D, E, F	IPR040351	Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P61006	rheumatoid arthritis astrocytic tumor plasma cell myeloma cancer psoriasis ovarian cancer
C, D, E, F	Pharos: Q96QF0	atrial fibrillation breast carcinoma gastric cancer large cell medulloblastoma medulloblastoma ovarian cancer pituitary cancer atypical teratoid rhabdoid tumor Crohn disease gastric carcinoma lung carcinoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis breast cancer atrial fibrillation breast carcinoma gastric cancer large cell medulloblastoma medulloblastoma ovarian cancer pituitary cancer atypical teratoid rhabdoid tumor Crohn disease gastric carcinoma lung carcinoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis breast cancer ductal breast carcinoma in situ invasive ductal breast carcinoma malignant ependymoma osteosarcoma pilocytic astrocytoma

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.