8SQZ

Structure of human ULK1 complex core (2:2:2 stoichiometry) in the PI3KC3-C1 mixture

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
C, D	PF12063	Atg1-like, MIT domain 1 (ATG1-like_MIT1)	Atg1-like, MIT domain 1	Members of this entry are serine/threonine-protein kinases and includes ATG1 from yeasts, Unc-51 from C. elegans and ULK1-2 from humans. ATG1 is required for vesicle formation in autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway [1,2]. U ...	Members of this entry are serine/threonine-protein kinases and includes ATG1 from yeasts, Unc-51 from C. elegans and ULK1-2 from humans. ATG1 is required for vesicle formation in autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway [1,2]. Unc-51 is important for axonal elongation and axonal guidance [4] and ULK1-2 are involved in autophagy in response to starvation [3]. They consist of a kinase domain at the N-terminal (Pfam:PF00069) and two tandem microtubule interacting and transport (MIT) domains (tMIT) at the C-terminal. MIT domains are known to mediate protein-protein interactions. In ATG1, MIT domains mediate the interaction with ATG13 [1]. In ULK1-2, MIT domains control the regulatory function and localization of the proteins and also mediate interactions with additional autophagy proteins [3]. This is the C-terminal MIT domain (MIT2).	Domain
C, D	PF21127	ATG1-like, MIT domain 2 (ATG1-like_MIT2)	ATG1-like, MIT domain 2	Members of this entry are serine/threonine-protein kinases and includes Atg1 from yeasts, Unc-51 from C. elegans and ULK1-2 from humans. Atg1 is required for vesicle formation in autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway [1,2]. ...	Members of this entry are serine/threonine-protein kinases and includes Atg1 from yeasts, Unc-51 from C. elegans and ULK1-2 from humans. Atg1 is required for vesicle formation in autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway [1,2]. Unc-51 is important for axonal elongation and axonal guidance [4,5] and ULK1-2 are involved in autophagy in response to starvation [3]. They consist of a kinase domain at the N-terminal (Pfam:PF00069) and two tandem microtubule interacting and transport (MIT) domains (tMIT) at the C-terminal which, in ATG1, mediates the interaction with ATG13 [1]. In ULK1-2, MIT domain control the regulatory function and localization of the proteins and also mediate interactions with additional autophagy proteins [3]. This is the C-terminal MIT domain (MIT2).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	RB1-inducible coiled-coil protein 1	protein-membrane adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding kinase binding enzyme binding protein kinase binding	catabolic process energy derivation by oxidation of organic compounds macroautophagy carbohydrate catabolic process autophagy macromolecule catabolic process cellular catabolic process polysaccharide metabolic process glucan metabolic process glycogen catabolic process process utilizing autophagic mechanism carbohydrate metabolic process glucan catabolic process glycogen metabolic process catabolic process energy derivation by oxidation of organic compounds macroautophagy carbohydrate catabolic process autophagy macromolecule catabolic process cellular catabolic process polysaccharide metabolic process glucan metabolic process glycogen catabolic process process utilizing autophagic mechanism carbohydrate metabolic process glucan catabolic process glycogen metabolic process cellular metabolic process primary metabolic process generation of precursor metabolites and energy glycophagy polysaccharide catabolic process metabolic process energy reserve metabolic process cellular process macromolecule metabolic process developmental process multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development heart development circulatory system development autophagosome assembly organelle assembly vacuole organization autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly cellular component organization or biogenesis piecemeal microautophagy of the nucleus microautophagy nucleophagy cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling biological regulation cell death extrinsic apoptotic signaling pathway cell communication apoptotic signaling pathway signal transduction apoptotic process programmed cell death ribophagy positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette positive regulation of cellular process regulation of signaling positive regulation of MAPK cascade regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication positive regulation of signaling negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of biological process negative regulation of signaling regulation of programmed cell death negative regulation of cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic process regulation of apoptotic signaling pathway positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of cellular metabolic process positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process organonitrogen compound metabolic process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process macromolecule modification regulation of phosphorus metabolic process regulation of phosphorylation regulation of metabolic process positive regulation of cell size regulation of cellular component size regulation of biological quality regulation of cell size regulation of anatomical structure size cellular biosynthetic process lipoprotein biosynthetic process lipoprotein metabolic process organonitrogen compound biosynthetic process protein lipidation regulation of lipoprotein metabolic process regulation of biosynthetic process regulation of protein lipidation macromolecule biosynthetic process regulation of cellular biosynthetic process biosynthetic process regulation of macromolecule biosynthetic process positive regulation of autophagy regulation of catabolic process regulation of autophagy positive regulation of catabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process cellular component disassembly organelle disassembly reticulophagy	membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane protein kinase complex membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex Atg1/ULK1 kinase complex cytoplasm transferase complex cytosol phagophore assembly site membrane phagophore assembly site lytic vacuole vacuole lysosome organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane vacuolar membrane autophagosome membrane autophagosome bounding membrane of organelle
C, D	Serine/threonine-protein kinase ULK1	small GTPase binding protein binding binding enzyme binding GTPase binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding small GTPase binding protein binding binding enzyme binding GTPase binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein-containing complex binding identical protein binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein serine/threonine kinase activity	multicellular organismal process regulation of growth regulation of cellular process axonogenesis regulation of cellular component size cell projection organization developmental growth negative regulation of biological process regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development multicellular organism development cell projection morphogenesis neuron differentiation multicellular organismal process regulation of growth regulation of cellular process axonogenesis regulation of cellular component size cell projection organization developmental growth negative regulation of biological process regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development multicellular organism development cell projection morphogenesis neuron differentiation negative regulation of growth neuron projection morphogenesis cell differentiation anatomical structure development regulation of biological quality system development developmental process regulation of biological process negative regulation of cellular component organization regulation of cell projection organization negative regulation of cell growth nervous system development developmental growth involved in morphogenesis generation of neurons negative regulation of axonogenesis negative regulation of developmental growth negative regulation of multicellular organismal process regulation of neuron projection development regulation of collateral sprouting regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis cellular component organization regulation of nervous system development neurogenesis negative regulation of neurogenesis regulation of extent of cell growth regulation of axonogenesis negative regulation of cellular process negative regulation of nervous system development regulation of multicellular organismal process negative regulation of cell differentiation cellular component organization or biogenesis negative regulation of cell projection organization regulation of anatomical structure morphogenesis regulation of cell size regulation of multicellular organismal development collateral sprouting regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth negative regulation of developmental process biological regulation growth axon development regulation of cell growth cell morphogenesis involved in neuron differentiation negative regulation of neuron projection development anatomical structure morphogenesis negative regulation of cell development neuron development cellular process negative regulation of collateral sprouting regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size protein localization localization cellular localization cellular macromolecule localization macromolecule localization catabolic process macroautophagy cellular metabolic process autophagy regulation of cellular metabolic process regulation of catabolic process regulation of autophagy cellular catabolic process regulation of macroautophagy regulation of cellular catabolic process metabolic process regulation of metabolic process process utilizing autophagic mechanism cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus piecemeal microautophagy of the nucleus microautophagy nucleophagy protein-containing complex organization regulation of cellular component biogenesis negative regulation of protein-containing complex assembly cellular component biogenesis regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly organonitrogen compound metabolic process protein phosphorylation phosphorylation primary metabolic process macromolecule modification peptidyl-amino acid modification phosphate-containing compound metabolic process peptidyl-threonine modification protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process peptidyl-threonine phosphorylation protein autophosphorylation peptidyl-serine modification peptidyl-serine phosphorylation axon extension neuron projection extension regulation of protein modification process cellular biosynthetic process lipoprotein biosynthetic process lipoprotein metabolic process organonitrogen compound biosynthetic process regulation of primary metabolic process protein lipidation regulation of lipoprotein metabolic process regulation of biosynthetic process regulation of protein lipidation regulation of protein metabolic process regulation of macromolecule metabolic process macromolecule biosynthetic process regulation of cellular biosynthetic process biosynthetic process regulation of macromolecule biosynthetic process positive regulation of organelle organization positive regulation of cellular component organization positive regulation of vacuole organization positive regulation of biological process autophagosome organization positive regulation of cellular metabolic process positive regulation of metabolic process positive regulation of autophagosome assembly positive regulation of macroautophagy positive regulation of cellular process positive regulation of autophagy autophagosome assembly organelle assembly vacuole organization positive regulation of cellular component biogenesis regulation of autophagosome assembly regulation of vacuole organization regulation of organelle organization positive regulation of catabolic process organelle organization regulation of organelle assembly positive regulation of cellular catabolic process positive regulation of organelle assembly signaling response to cytokine regulation of signal transduction cytokine-mediated signaling pathway cell communication cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus signal transduction regulation of signaling regulation of tumor necrosis factor-mediated signaling pathway cell surface receptor signaling pathway regulation of cytokine-mediated signaling pathway response to peptide regulation of response to cytokine stimulus regulation of response to stimulus response to chemical regulation of cell communication response to tumor necrosis factor regeneration neuron projection regeneration cellular response to stress response to stress response to starvation negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation cellular component disassembly organelle disassembly reticulophagy	protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex intracellular anatomical structure catalytic complex serine/threonine protein kinase complex Atg1/ULK1 kinase complex cytoplasm cellular anatomical entity transferase complex cytosol membrane-bounded organelle intracellular organelle organelle protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex intracellular anatomical structure catalytic complex serine/threonine protein kinase complex Atg1/ULK1 kinase complex cytoplasm cellular anatomical entity transferase complex cytosol membrane-bounded organelle intracellular organelle organelle vacuole autophagosome intracellular membrane-bounded organelle vacuolar membrane autophagosome membrane membrane bounding membrane of organelle organelle membrane endosome intracellular vesicle recycling endosome endomembrane system cytoplasmic vesicle vesicle mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane axon cell projection neuron projection plasma membrane bounded cell projection phagophore assembly site phagophore assembly site membrane organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane omegasome membrane omegasome
E, F	Autophagy-related protein 13	protein binding binding kinase binding enzyme binding protein kinase binding enzyme regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity protein serine/threonine kinase activator activity kinase activator activity enzyme activator activity molecular function activator activity protein kinase activator activity	negative regulation of cell population proliferation regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation negative regulation of cellular process biological regulation negative regulation of biological process cellular process autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy negative regulation of cell population proliferation regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation negative regulation of cellular process biological regulation negative regulation of biological process cellular process autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy cellular metabolic process autophagy autophagosome organization cellular component biogenesis cellular component organization cellular catabolic process organelle organization cellular component assembly metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism piecemeal microautophagy of the nucleus microautophagy nucleophagy regulation of protein modification process cellular biosynthetic process lipoprotein biosynthetic process lipoprotein metabolic process organonitrogen compound biosynthetic process regulation of primary metabolic process protein lipidation regulation of lipoprotein metabolic process protein metabolic process protein modification process regulation of biosynthetic process regulation of protein lipidation organonitrogen compound metabolic process regulation of protein metabolic process regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process macromolecule biosynthetic process regulation of cellular biosynthetic process biosynthetic process macromolecule modification regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process cellular response to stimulus cellular response to stress response to stimulus response to mitochondrial depolarisation response to stress cellular component disassembly mitophagy organelle disassembly autophagy of mitochondrion mitochondrion organization positive regulation of autophagy positive regulation of biological process positive regulation of cellular metabolic process regulation of catabolic process regulation of autophagy positive regulation of catabolic process positive regulation of metabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process positive regulation of cellular process protein localization regulation of localization establishment of protein localization cellular localization regulation of protein localization protein targeting regulation of protein targeting to mitochondrion positive regulation of establishment of protein localization localization cellular macromolecule localization positive regulation of protein targeting to mitochondrion regulation of establishment of protein localization establishment of localization regulation of establishment of protein localization to mitochondrion establishment of protein localization to organelle regulation of protein targeting regulation of cellular localization macromolecule localization protein localization to organelle protein localization to mitochondrion positive regulation of protein localization protein targeting to mitochondrion establishment of protein localization to mitochondrion positive regulation of establishment of protein localization to mitochondrion protein localization to phagophore assembly site	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle vacuole autophagosome protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle vacuole autophagosome protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex Atg1/ULK1 kinase complex transferase complex cytosol phagophore assembly site membrane membrane phagophore assembly site organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR019460	Autophagy-related protein 11, C-terminal	Domain
A, B	IPR040040	Autophagy-related protein 11	Family
C, D	IPR045269	Serine/threonine-protein kinase Atg1-like	Family
C, D	IPR000719	Protein kinase domain	Domain
C, D	IPR048941	ATG1-like, MIT domain 2	Domain
C, D	IPR016237	Serine/threonine-protein kinase, Ulk1/Ulk2	Family
C, D	IPR017441	Protein kinase, ATP binding site	Binding Site
C, D	IPR022708	Serine/threonine-protein kinase Atg1-like, tMIT domain	Domain
C, D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
C, D	IPR008271	Serine/threonine-protein kinase, active site	Active Site
E, F	IPR036570	HORMA domain superfamily	Homologous Superfamily
E, F	IPR040182	Autophagy-related protein 13	Family
E, F	IPR018731	Autophagy-related protein 13, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q8TDY2	schizophrenia breast carcinoma Alzheimer disease breast adenocarcinoma glioblastoma limb-girdle muscular dystrophy Malignant neoplasm of breast ovarian cancer astrocytic tumor breast cancer hereditary breast carcinoma malignant glioma plasma cell myeloma spina bifida atypical teratoid rhabdoid tumor schizophrenia breast carcinoma Alzheimer disease breast adenocarcinoma glioblastoma limb-girdle muscular dystrophy Malignant neoplasm of breast ovarian cancer astrocytic tumor breast cancer hereditary breast carcinoma malignant glioma plasma cell myeloma spina bifida atypical teratoid rhabdoid tumor hereditary spastic paraplegia malignant mesothelioma sarcoidosis
C, D	Pharos: O75385	gastrointestinal stromal tumor malignant glioma Pancreatic Neuroendocrine Tumor subependymal giant cell astrocytoma lung adenocarcinoma osteosarcoma pilocytic astrocytoma thrombocytopenia due to immune destruction malignant ependymoma ovarian mucinous adenocarcinoma renal cell carcinoma
E, F	Pharos: O75143	atypical teratoid rhabdoid tumor lung cancer psoriasis autism spectrum disorder osteoarthritis vascular disease large cell medulloblastoma pancreatic intraductal papillary-mucinous 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 R01GM133198.