9CE3 | pdb_00009ce3

Structure of the TSC:WIPI3 lysosomal recruitment complex

External Resource: Annotation

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
F	PF21032	PROPPIN (PROPPIN)	PROPPIN	-	Repeat
E	PF00566	Rab-GTPase-TBC domain (RabGAP-TBC)	Rab-GTPase-TBC domain	-	Family
C, D	PF04388	Hamartin protein (Hamartin)	Hamartin protein	-	Family
A, B	PF03542	Tuberin (Tuberin)	Tuberin	-	Family
A, B	PF02145	Rap/ran-GAP (Rap_GAP)	Rap/ran-GAP		Domain
A, B	PF11864	Domain of unknown function (DUF3384) (DUF3384)	Domain of unknown function (DUF3384)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G, H	Unknown fragment	-	-	-
F	WD repeat domain phosphoinositide-interacting protein 3	phosphatidylinositol-3,5-bisphosphate binding binding ion binding anion binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding small molecule binding phosphatidylinositol-3-phosphate binding protein-containing complex binding TSC1-TSC2 complex binding protein-macromolecule adaptor activity phosphatidylinositol-3,5-bisphosphate binding binding ion binding anion binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding small molecule binding phosphatidylinositol-3-phosphate binding protein-containing complex binding TSC1-TSC2 complex binding protein-macromolecule adaptor activity molecular adaptor activity	carbohydrate metabolic process catabolic process glucan catabolic process energy derivation by oxidation of organic compounds macroautophagy glycogen metabolic process carbohydrate catabolic process autophagy primary metabolic process generation of precursor metabolites and energy macromolecule catabolic process polysaccharide metabolic process glucan metabolic process glycogen catabolic process glycophagy carbohydrate metabolic process catabolic process glucan catabolic process energy derivation by oxidation of organic compounds macroautophagy glycogen metabolic process carbohydrate catabolic process autophagy primary metabolic process generation of precursor metabolites and energy macromolecule catabolic process polysaccharide metabolic process glucan metabolic process glycogen catabolic process glycophagy polysaccharide catabolic process metabolic process cellular process energy reserve metabolic process macromolecule metabolic process process utilizing autophagic mechanism cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress response to starvation cellular response to starvation autophagy of mitochondrion autophagosome assembly organelle assembly vacuole organization autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly cellular component organization or biogenesis nucleophagy autophagy of peroxisome pexophagy localization macromolecule localization protein localization to phagophore assembly site intracellular protein localization	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol phagophore assembly site membrane membrane phagophore assembly site membrane-bounded organelle intracellular organelle organelle lytic vacuole vacuole intracellular membrane-bounded organelle lysosome
E	TBC1 domain family member 7	small GTPase binding protein binding binding enzyme binding GTPase binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity protein-containing complex binding TSC1-TSC2 complex binding	cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress cellular process response to starvation cellular response to starvation regulation of cellular process negative regulation of signaling signaling negative regulation of intracellular signal transduction negative regulation of biological process cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress cellular process response to starvation cellular response to starvation regulation of cellular process negative regulation of signaling signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction negative regulation of cell communication intracellular signal transduction cell communication negative regulation of TOR signaling regulation of intracellular signal transduction negative regulation of cellular process signal transduction TOR signaling regulation of signaling regulation of biological process regulation of TOR signaling negative regulation of response to stimulus biological regulation negative regulation of signal transduction regulation of response to stimulus regulation of cell communication response to endogenous stimulus response to growth factor negative regulation of TORC1 signaling regulation of TORC1 signaling TORC1 signaling positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity activation of GTPase activity regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process protein ubiquitination positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process macromolecule modification metabolic process macromolecule metabolic process post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of cellular component organization cell projection organization negative regulation of organelle assembly plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization negative regulation of plasma membrane bounded cell projection assembly cellular component assembly cilium assembly cellular component organization or biogenesis negative regulation of cell projection organization cilium organization organelle assembly plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis regulation of organelle organization regulation of plasma membrane bounded cell projection assembly organelle organization regulation of cilium assembly negative regulation of organelle organization regulation of organelle assembly negative regulation of cilium assembly cell projection assembly regulation of plasma membrane bounded cell projection organization	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle protein-containing complex TSC1-TSC2 complex cytosol vacuolar membrane membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle protein-containing complex TSC1-TSC2 complex cytosol vacuolar membrane membrane lytic vacuole vacuole lytic vacuole membrane bounding membrane of organelle lysosomal membrane organelle membrane lysosome intracellular membraneless organelle cilium plasma membrane bounded cell projection ciliary basal body cell projection microtubule organizing center cytoskeleton membraneless organelle microtubule cytoskeleton
C, D	Hamartin	molecular function inhibitor activity molecular function regulator activity ATPase inhibitor activity ATPase regulator activity protein binding binding protein-folding chaperone binding Hsp90 protein binding heat shock protein binding Hsp70 protein binding protein folding chaperone	D-glucose import hexose transmembrane transport transport carbohydrate transport establishment of localization transmembrane transport localization D-glucose transmembrane transport cellular process monosaccharide transmembrane transport carbohydrate transmembrane transport regulation of protein stability biological regulation regulation of biological quality D-glucose import hexose transmembrane transport transport carbohydrate transport establishment of localization transmembrane transport localization D-glucose transmembrane transport cellular process monosaccharide transmembrane transport carbohydrate transmembrane transport regulation of protein stability biological regulation regulation of biological quality protein stabilization response to stimulus immune response immune system process adaptive immune response cell population proliferation developmental process heart development multicellular organismal process cellular developmental process cardiac muscle tissue development cardiac muscle cell differentiation animal organ development muscle cell differentiation tissue development cardiocyte differentiation striated muscle tissue development circulatory system development muscle structure development multicellular organism development cell differentiation anatomical structure development striated muscle cell differentiation muscle tissue development system development negative regulation of ATP-dependent activity regulation of ATP-dependent activity regulation of molecular function negative regulation of molecular function regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization cell-substrate junction assembly positive regulation of cell-substrate junction organization positive regulation of biological process cellular component organization cellular component biogenesis cell adhesion cellular component assembly cell junction assembly positive regulation of cell-substrate adhesion regulation of cell-substrate junction organization cellular component organization or biogenesis positive regulation of cellular process focal adhesion assembly regulation of biological process positive regulation of focal adhesion assembly positive regulation of cellular component biogenesis regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion cell-substrate adhesion positive regulation of cell-matrix adhesion regulation of cellular component biogenesis regulation of cell junction assembly positive regulation of cell junction assembly cell junction organization cell-matrix adhesion regulation of cell-matrix adhesion cell-substrate junction organization regulation of focal adhesion assembly regulation of cell-substrate junction assembly cellular response to stimulus cellular response to nutrient levels response to nutrient levels cellular response to stress response to stress response to starvation cellular response to starvation embryonic epithelial tube formation chordate embryonic development tube formation embryo development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching epithelial tube morphogenesis morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium nervous system development anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure head development forebrain development brain development pallium development cerebral cortex development central nervous system development telencephalon development negative regulation of signaling signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction negative regulation of cell communication intracellular signal transduction cell communication negative regulation of TOR signaling regulation of intracellular signal transduction negative regulation of cellular process signal transduction TOR signaling regulation of signaling regulation of TOR signaling negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus regulation of cell communication kidney development renal system development hippocampus development limbic system development adult locomotory behavior behavior adult behavior locomotory behavior immunological memory formation process cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation cell activation involved in immune response leukocyte activation memory T cell differentiation T cell activation involved in immune response T cell activation leukocyte activation involved in immune response T cell differentiation lymphocyte activation involved in immune response hemopoiesis cell activation T cell differentiation involved in immune response immune effector process immunological memory process leukocyte differentiation regulation of cytoskeleton organization regulation of actin filament-based process regulation of actin filament bundle assembly actin filament bundle organization actin filament-based process stress fiber assembly regulation of actin filament organization actin cytoskeleton organization actomyosin structure organization actin filament organization regulation of organelle organization regulation of stress fiber assembly organelle organization contractile actin filament bundle assembly regulation of actomyosin structure organization regulation of actin cytoskeleton organization actin filament bundle assembly regulation of supramolecular fiber organization supramolecular fiber organization cytoskeleton organization negative regulation of catabolic process catabolic process macroautophagy negative regulation of metabolic process autophagy regulation of catabolic process regulation of autophagy negative regulation of macroautophagy regulation of macroautophagy negative regulation of autophagy metabolic process process utilizing autophagic mechanism regulation of metabolic process synapse organization monoatomic ion transport potassium ion transport monoatomic cation transport metal ion transport response to decreased oxygen levels cellular response to chemical stimulus cellular response to oxygen levels response to chemical response to oxygen levels cellular response to decreased oxygen levels response to abiotic stimulus negative regulation of cell population proliferation regulation of cell population proliferation response to hormone response to endogenous stimulus response to peptide hormone response to insulin response to oxygen-containing compound response to nitrogen compound negative regulation of TORC1 signaling regulation of TORC1 signaling TORC1 signaling system process learning learning or memory nervous system process cognition associative learning activation of GTPase activity positive regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity myelination axon ensheathment ensheathment of neurons cell cycle regulation of cell cycle cell projection organization negative regulation of cell size regulation of cellular component size regulation of cell size regulation of anatomical structure size	cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium membrane intracellular anatomical structure cytoplasm cytosol protein-containing complex protein folding chaperone complex intracellular protein-containing complex vacuolar membrane membrane-bounded organelle cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium membrane intracellular anatomical structure cytoplasm cytosol protein-containing complex protein folding chaperone complex intracellular protein-containing complex vacuolar membrane membrane-bounded organelle lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane organelle membrane lysosome perinuclear region of cytoplasm intracellular membraneless organelle cilium ciliary basal body microtubule organizing center cytoskeleton membraneless organelle microtubule cytoskeleton TSC1-TSC2 complex cell periphery cell cortex plasma membrane lipid droplet postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization synapse cell junction asymmetric synapse nucleus
A, B	Isoform 4 of Tuberin	small GTPase binding protein binding binding enzyme binding GTPase binding Hsp90 protein binding heat shock protein binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity small GTPase binding protein binding binding enzyme binding GTPase binding Hsp90 protein binding heat shock protein binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity identical protein binding protein homodimerization activity protein dimerization activity phosphatase binding	catabolic process regulation of cellular process macroautophagy autophagy negative regulation of biological process regulation of autophagy mitophagy negative regulation of cellular process regulation of autophagy of mitochondrion process utilizing autophagic mechanism negative regulation of catabolic process regulation of biological process negative regulation of metabolic process negative regulation of autophagy of mitochondrion catabolic process regulation of cellular process macroautophagy autophagy negative regulation of biological process regulation of autophagy mitophagy negative regulation of cellular process regulation of autophagy of mitochondrion process utilizing autophagic mechanism negative regulation of catabolic process regulation of biological process negative regulation of metabolic process negative regulation of autophagy of mitochondrion biological regulation regulation of mitophagy regulation of catabolic process negative regulation of mitophagy negative regulation of macroautophagy regulation of macroautophagy negative regulation of autophagy cellular process metabolic process regulation of metabolic process autophagy of mitochondrion developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development cellular response to stimulus response to stimulus negative regulation of signaling signaling regulation of signal transduction negative regulation of cell communication cell communication negative regulation of Wnt signaling pathway signal transduction Wnt signaling pathway regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus regulation of cell communication localization macromolecule localization intracellular protein localization regulation of localization import into cell regulation of cellular component organization regulation of transport transport regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport cellular component organization cellular component organization or biogenesis endocytosis regulation of endocytosis positive chemotaxis chemotaxis taxis response to chemical response to external stimulus locomotion establishment of protein localization cellular localization nitrogen compound transport nucleocytoplasmic transport nuclear transport intracellular transport protein localization to nucleus import into nucleus establishment of protein localization to organelle protein transport establishment of localization in cell protein localization to organelle protein import into nucleus intracellular protein transport cellular response to nitrogen compound response to peptide hormone insulin receptor signaling pathway regulation of cellular response to insulin stimulus cell surface receptor protein tyrosine kinase signaling pathway cellular response to endogenous stimulus response to hormone enzyme-linked receptor protein signaling pathway cellular response to hormone stimulus response to endogenous stimulus regulation of insulin receptor signaling pathway response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus negative regulation of cellular response to insulin stimulus negative regulation of insulin receptor signaling pathway response to insulin cellular response to insulin stimulus cellular response to nutrient levels response to nutrient levels cellular response to stress response to stress response to starvation cellular response to starvation embryonic epithelial tube formation chordate embryonic development tube formation embryo development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching epithelial tube morphogenesis morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium nervous system development tissue development anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure negative regulation of intracellular signal transduction intracellular signal transduction negative regulation of TOR signaling regulation of intracellular signal transduction TOR signaling regulation of TOR signaling positive regulation of autophagy positive regulation of biological process positive regulation of catabolic process positive regulation of metabolic process positive regulation of macroautophagy positive regulation of cellular process negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction intracellular signaling cassette phosphatidylinositol 3-kinase/protein kinase B signal transduction small GTPase-mediated signal transduction regulation of small GTPase mediated signal transduction negative regulation of TORC1 signaling regulation of TORC1 signaling TORC1 signaling cell cycle regulation of cell cycle anoikis apoptotic process cell death programmed cell death	protein-containing complex cellular anatomical structure intracellular anatomical structure TSC1-TSC2 complex cytoplasm cytosol membrane membrane-bounded organelle intracellular organelle organelle lytic vacuole vacuole intracellular membrane-bounded organelle lysosome protein-containing complex cellular anatomical structure intracellular anatomical structure TSC1-TSC2 complex cytoplasm cytosol membrane membrane-bounded organelle intracellular organelle organelle lytic vacuole vacuole intracellular membrane-bounded organelle lysosome vacuolar membrane lytic vacuole membrane bounding membrane of organelle lysosomal membrane organelle membrane Golgi apparatus endomembrane system postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization synapse cell junction asymmetric synapse perinuclear region of cytoplasm nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F	IPR048720	PROPPIN	Family
F	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
F	IPR001680	WD40 repeat	Repeat
F	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
E	IPR035969	Rab-GAP-TBC domain superfamily	Homologous Superfamily
E	IPR043039	TBC1 domain family member 7, domain 2	Homologous Superfamily
E	IPR039842	TBC1 domain family member 7	Family
E	IPR000195	Rab-GAP-TBC domain	Domain
C, D	IPR007483	Hamartin	Family
A, B	IPR016024	Armadillo-type fold	Homologous Superfamily
A, B	IPR011989	Armadillo-like helical	Homologous Superfamily
A, B	IPR024584	Tuberin, N-terminal	Domain
A, B	IPR000331	Rap/Ran-GAP domain	Domain
A, B	IPR027107	Tuberin/Ral GTPase-activating protein subunit alpha	Family
A, B	IPR018515	Tuberin-type domain	Domain
A, B	IPR035974	Rap/Ran-GAP superfamily	Homologous Superfamily
A, B	IPR003913	Tuberin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
F	Pharos: Q5MNZ6	intellectual disability epilepsy Mental deficiency ovarian cancer psoriasis plasma cell myeloma neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures
E	Pharos: Q9P0N9	acute myeloid leukemia Macrocephaly ovarian cancer tuberculosis hydrocephalus macrocephaly/megalencephaly syndrome, autosomal recessive pancreatic ductal adenocarcinoma invasive ductal breast carcinoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma
C, D	Pharos: Q92574	tuberous sclerosis lung lymphangioleiomyomatosis squamous cell carcinoma renal cell carcinoma epilepsy progressive myoclonus epilepsy isolated focal cortical dysplasia type II tuberous sclerosis 1 Cognition Disorders dentatorubral-pallidoluysian atrophy West syndrome brain disease chromophobe renal cell carcinoma collecting duct carcinoma lymphangioleiomyomatosis tuberous sclerosis lung lymphangioleiomyomatosis squamous cell carcinoma renal cell carcinoma epilepsy progressive myoclonus epilepsy isolated focal cortical dysplasia type II tuberous sclerosis 1 Cognition Disorders dentatorubral-pallidoluysian atrophy West syndrome brain disease chromophobe renal cell carcinoma collecting duct carcinoma lymphangioleiomyomatosis developmental and epileptic encephalopathy sarcomatoid renal cell carcinoma visual epilepsy papillary renal cell carcinoma intellectual disability malignant ependymoma urinary bladder neoplasm neoplasm angiomyolipoma atypical teratoid rhabdoid tumor oral cavity neoplasm hepatocellular carcinoma large cell medulloblastoma malignant glioma urinary bladder cancer action myoclonus-renal failure syndrome ovarian cancer renal carcinoma bladder benign neoplasm glioblastoma cancer clear cell renal carcinoma Spasmus nutans Ehlers-Danlos syndrome urinary bladder carcinoma adult hepatocellular carcinoma autism benign urinary system neoplasm bladder carcinoma in situ cholangiocarcinoma
A, B	Pharos: P49815	tuberous sclerosis squamous cell carcinoma lung lymphangioleiomyomatosis epilepsy tuberous sclerosis 2 acute myeloid leukemia cancer lymphangioleiomyomatosis Mouth Neoplasms autosomal dominant polycystic kidney disease type 1 with tuberous sclerosis intellectual disability brain disease leiomyoma visual epilepsy autism tuberous sclerosis squamous cell carcinoma lung lymphangioleiomyomatosis epilepsy tuberous sclerosis 2 acute myeloid leukemia cancer lymphangioleiomyomatosis Mouth Neoplasms autosomal dominant polycystic kidney disease type 1 with tuberous sclerosis intellectual disability brain disease leiomyoma visual epilepsy autism isolated focal cortical dysplasia type II kidney cancer developmental and epileptic encephalopathy uterine corpus leiomyoma West syndrome kidney neoplasm subependymal giant cell astrocytoma dilated cardiomyopathy pancreatic neoplasm astrocytic tumor head and neck squamous cell carcinoma Spasmus nutans Ehlers-Danlos syndrome tuberous sclerosis 1 oral cavity neoplasm adult hepatocellular carcinoma precancerous condition thyroid gland carcinoma malignant pancreatic neoplasm ovarian cancer angiomyolipoma atrial fibrillation benign urinary system neoplasm

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.