8JC5 | pdb_00008jc5

Crystal structure of PLEKHM1 RUN domain in complex with GTP-bound Arl8b(Q75L)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

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	8061451	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8061451	3002022	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF02759	RUN domain (RUN)	RUN domain	-	Family
A, B	PF00025	ADP-ribosylation factor family (Arf)	ADP-ribosylation factor family	Pfam combines a number of different Prosite families together	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Pleckstrin homology domain-containing family M member 1	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion cellular process metabolic process cellular component organization or biogenesis vesicle fusion process utilizing autophagic mechanism cellular localization late endosome to lysosome transport establishment of localization in cell vacuolar transport intracellular transport lysosomal transport organelle localization lysosome localization vacuolar localization establishment of protein localization nitrogen compound transport protein transport macromolecule localization intracellular protein localization multicellular organismal process regulation of biological process homeostatic process biological regulation positive regulation of biological process regulation of bone remodeling tissue homeostasis regulation of tissue remodeling regulation of bone resorption bone resorption multicellular organismal-level homeostasis tissue remodeling bone remodeling anatomical structure homeostasis positive regulation of multicellular organismal process regulation of multicellular organismal process positive regulation of bone resorption regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization cell projection organization ruffle organization plasma membrane bounded cell projection assembly ruffle assembly cellular component biogenesis cellular component assembly positive regulation of cell projection organization positive regulation of cellular process plasma membrane bounded cell projection organization positive regulation of cellular component biogenesis regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis positive regulation of ruffle assembly regulation of plasma membrane bounded cell projection assembly regulation of ruffle assembly cell projection assembly regulation of plasma membrane bounded cell projection organization positive regulation of plasma membrane bounded cell projection assembly	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen vacuolar membrane autolysosome membrane lytic vacuole vacuole autolysosome membrane lytic vacuole membrane bounding membrane of organelle lysosomal membrane secondary lysosome cytoplasm organelle membrane lysosome endosome membrane endosome intracellular vesicle late endosome membrane endomembrane system cytoplasmic vesicle membrane cytoplasmic vesicle vesicle membrane late endosome vesicle nucleoplasm
A, B	ADP-ribosylation factor-like protein 8B	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 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 protein binding tubulin binding alpha-tubulin binding GDP 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 beta-tubulin binding	exit from host cell biological process involved in interspecies interaction between organisms non-lytic viral release viral process viral exocytosis viral release from host cell viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction membrane organization catabolic process transport macroautophagy membrane fusion exit from host cell biological process involved in interspecies interaction between organisms non-lytic viral release viral process viral exocytosis viral release from host cell viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion cellular process metabolic process cellular component organization or biogenesis vesicle fusion process utilizing autophagic mechanism import into cell cellular component biogenesis lysosome organization cellular component assembly phagolysosome assembly phagocytosis vacuole organization organelle assembly lytic vacuole organization phagosome-lysosome fusion phagosome maturation endocytosis early endosome to Golgi transport cellular localization intracellular transport endosomal transport cytosolic transport retrograde transport, endosome to Golgi establishment of localization in cell Golgi vesicle transport anterograde axonal transport axonal transport axo-dendritic transport microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process cell division cell cycle chromosome segregation cell cycle process organelle localization lysosome localization vacuolar localization establishment of protein localization nitrogen compound transport protein transport macromolecule localization intracellular protein localization protein localization to endosome protein localization to organelle protein localization to early endosome antigen processing and presentation antigen processing and presentation of peptide or polysaccharide antigen via MHC class II immune system process antigen processing and presentation of polysaccharide antigen via MHC class II antigen processing and presentation following phagocytosis lymphocyte mediated immunity response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus leukocyte mediated cytotoxicity response to biotic stimulus immune effector process defense response to other organism response to stress natural killer cell mediated cytotoxicity innate immune response leukocyte mediated immunity response to external biotic stimulus natural killer cell mediated immunity cell killing regulated exocytosis secretion export from cell calcium ion regulated lysosome exocytosis secretion by cell exocytosis calcium-ion regulated exocytosis late endosome to lysosome transport vacuolar transport lysosomal transport wound healing plasma membrane repair plasma membrane organization response to wounding endomembrane system organization endosome to lysosome transport intracellular cholesterol transport vesicle-mediated cholesterol transport organic hydroxy compound transport intracellular sterol transport sterol transport intracellular lipid transport endosome to lysosome transport of low-density lipoprotein particle lipid localization lipid transport cholesterol transport	midbody cellular anatomical structure membrane intracellular organelle intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle midzone microtubule cytoskeleton extracellular exosome membrane-bounded organelle midbody cellular anatomical structure membrane intracellular organelle intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle midzone microtubule cytoskeleton extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytoplasm cytosol endosome membrane endosome intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane late endosome organelle membrane lytic vacuole vacuole lysosome vacuolar membrane lytic vacuole membrane lysosomal membrane cytolytic granule cytolytic granule membrane early endosome early endosome membrane synapse cell junction neuron projection cytoplasm axon axon cytoplasm neuron projection cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection cell projection

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR037213	RUN domain superfamily	Homologous Superfamily
C, D	IPR025258	Rubicon Homology Domain	Domain
C, D	IPR004012	RUN domain	Domain
C, D	IPR002219	Protein kinase C-like, phorbol ester/diacylglycerol-binding domain	Domain
C, D	IPR001849	Pleckstrin homology domain	Domain
C, D	IPR047326	PLEKHM1, RUN domain	Domain
C, D	IPR042827	PLEKHM1, PH domain	Domain
C, D	IPR011993	PH-like domain superfamily	Homologous Superfamily
C, D	IPR051366	Differentially Expressed in FDCP 8 Homolog	Family
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR005225	Small GTP-binding domain	Domain
A, B	IPR044154	ADP-ribosylation factor-like protein 8A/8B	Family
A, B	IPR006689	Small GTPase superfamily, ARF/SAR type	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: Q9Y4G2	osteopetrosis autosomal recessive osteopetrosis 6 allergic rhinitis endogenous depression osteosarcoma systemic lupus erythematosus atypical teratoid rhabdoid tumor large cell medulloblastoma Osteopetrosis - intermediate type ovarian cancer lung cancer osteopetrosis, autosomal dominant 3 ovarian carcinoma
A, B	Pharos: Q9NVJ2	atypical teratoid rhabdoid tumor dermatomyositis large cell medulloblastoma medulloblastoma Pick disease tuberculosis breast cancer glioblastoma lymphoplasmacytic lymphoma ovarian cancer plasma cell myeloma breast carcinoma invasive ductal breast carcinoma malignant pancreatic neoplasm pancreatic ductal adenocarcinoma atypical teratoid rhabdoid tumor dermatomyositis large cell medulloblastoma medulloblastoma Pick disease tuberculosis breast cancer glioblastoma lymphoplasmacytic lymphoma ovarian cancer plasma cell myeloma breast carcinoma invasive ductal breast carcinoma malignant pancreatic neoplasm pancreatic ductal adenocarcinoma primitive neuroectodermal tumor

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.