6EMK | pdb_00006emk

Cryo-EM Structure of Saccharomyces cerevisiae Target of Rapamycin Complex 2

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G	SCOP2 Family	Ankyrin repeat	8082137	4000366	SCOP2 (2022-06-29)
G	SCOP2 Superfamily	Ankyrin repeat	8082138	3000154	SCOP2 (2022-06-29)
H	SCOP2B Superfamily	Ankyrin repeat	8082138	3000154	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)
J	ATP-synt_Eps	e6emkJ1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
I		e6emkI1	A: a/b three-layered sandwiches	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F:	ECOD (v294.1)
G		e6emkG1	A: a/b three-layered sandwiches	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F:	ECOD (v294.1)
H	ATP-synt_Eps	e6emkH1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
D	ATP-synt_Eps	e6emkD1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
B		e6emkB1	A: a/b three-layered sandwiches	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F:	ECOD (v294.1)
A	ABC_membrane	e6emkA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ABC_membrane	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G, H	PF00023	Ankyrin repeat (Ank)	Ankyrin repeat	-	Repeat
B, D	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat
A, C	PF02260	FATC domain (FATC)	FATC domain	-	Family
A, C	PF23593	Serine/threonine-protein kinase ATR-like, HEAT repeats (HEAT_ATR)	Serine/threonine-protein kinase ATR-like, HEAT repeats	-	Repeat
A, C	PF08771	FKBP12-rapamycin binding domain (FRB_dom)	FKBP12-rapamycin binding domain	The macrolide antibiotic rapamycin and the cytosol protein FKBP12 can form a complex which specifically inhibits the TORC1 complex, leading to growth arrest. The FKBP12-rapamycin complex interferes with TORC1 function by binding to the FKBP12-rapa ...	The macrolide antibiotic rapamycin and the cytosol protein FKBP12 can form a complex which specifically inhibits the TORC1 complex, leading to growth arrest. The FKBP12-rapamycin complex interferes with TORC1 function by binding to the FKBP12-rapamycin binding domain (FRB) of the TOR proteins. This entry represents the FRB domain [1, 2].	Domain
A, C	PF00454	Phosphatidylinositol 3- and 4-kinase (PI3_PI4_kinase)	Phosphatidylinositol 3- and 4-kinase	-	Family
A, C	PF11865	Serine/threonine-protein kinase mTOR domain (mTOR_dom)	Serine/threonine-protein kinase mTOR domain	-	Repeat
A, C	PF02259	FAT domain (FAT)	FAT domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I, J	Target of rapamycin complex 2 subunit AVO1	ion binding binding phosphatidylinositol-4,5-bisphosphate binding anion binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding small molecule binding molecular adaptor activity	cellular response to stimulus TOR signaling regulation of biological process regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication TORC2 signaling cellular process signal transduction cellular component organization establishment or maintenance of actin cytoskeleton polarity cellular response to stimulus TOR signaling regulation of biological process regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication TORC2 signaling cellular process signal transduction cellular component organization establishment or maintenance of actin cytoskeleton polarity organelle organization establishment or maintenance of cytoskeleton polarity actin cytoskeleton organization actin filament-based process cellular component organization or biogenesis establishment or maintenance of cell polarity cytoskeleton organization regulation of growth regulation of cellular component organization growth regulation of cell growth cell growth	cell periphery cellular anatomical structure plasma membrane membrane vacuolar membrane membrane-bounded organelle intracellular anatomical structure vacuole intracellular membrane-bounded organelle intracellular organelle bounding membrane of organelle organelle cytoplasm organelle membrane cell periphery cellular anatomical structure plasma membrane membrane vacuolar membrane membrane-bounded organelle intracellular anatomical structure vacuole intracellular membrane-bounded organelle intracellular organelle bounding membrane of organelle organelle cytoplasm organelle membrane TORC2 complex protein-containing complex TOR complex intracellular protein-containing complex
G, H	Target of rapamycin complex 2 subunit AVO2	-	cellular response to stimulus TOR signaling regulation of biological process regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication cellular process signal transduction regulation of growth regulation of cellular component organization growth cellular response to stimulus TOR signaling regulation of biological process regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication cellular process signal transduction regulation of growth regulation of cellular component organization growth regulation of cell growth cell growth cellular component organization cellular component organization or biogenesis establishment or maintenance of actin cytoskeleton polarity organelle organization establishment or maintenance of cytoskeleton polarity actin cytoskeleton organization actin filament-based process establishment or maintenance of cell polarity cytoskeleton organization	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane vacuolar membrane membrane-bounded organelle vacuole intracellular membrane-bounded organelle intracellular organelle bounding membrane of organelle organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane vacuolar membrane membrane-bounded organelle vacuole intracellular membrane-bounded organelle intracellular organelle bounding membrane of organelle organelle organelle membrane nucleus TORC2 complex protein-containing complex TOR complex intracellular protein-containing complex
E, F	Target of rapamycin complex 2 subunit TSC11	-	-	-
B, D	Target of rapamycin complex subunit LST8	enzyme regulator activity protein serine/threonine kinase activator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity	cellular component organization establishment or maintenance of actin cytoskeleton polarity organelle organization establishment or maintenance of cytoskeleton polarity actin cytoskeleton organization actin filament-based process cellular process cellular component organization or biogenesis establishment or maintenance of cell polarity cytoskeleton organization regulation of cytoskeleton organization regulation of biological process regulation of cellular component organization regulation of cellular process cellular component organization establishment or maintenance of actin cytoskeleton polarity organelle organization establishment or maintenance of cytoskeleton polarity actin cytoskeleton organization actin filament-based process cellular process cellular component organization or biogenesis establishment or maintenance of cell polarity cytoskeleton organization regulation of cytoskeleton organization regulation of biological process regulation of cellular component organization regulation of cellular process regulation of actin filament-based process biological regulation regulation of organelle organization regulation of actin cytoskeleton organization fungal-type cell wall organization fungal-type cell wall organization or biogenesis cell wall organization or biogenesis cell wall organization external encapsulating structure organization cellular response to stimulus TOR signaling response to stimulus signaling intracellular signal transduction cell communication signal transduction regulation of growth growth regulation of cell growth cell growth cell cycle regulation of cell cycle response to nutrient levels response to chemical response to nutrient mitochondria-nucleus signaling pathway	membrane-bounded organelle Golgi membrane intracellular anatomical structure Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle cellular anatomical structure organelle cytoplasm organelle membrane cytosol membrane-bounded organelle Golgi membrane intracellular anatomical structure Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle cellular anatomical structure organelle cytoplasm organelle membrane cytosol endosome membrane endosome intracellular vesicle cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle vesicle cell periphery plasma membrane vacuolar membrane vacuole nucleus membrane-enclosed lumen intracellular organelle lumen organelle lumen nuclear periphery nuclear lumen protein-containing complex TORC1 complex TOR complex intracellular protein-containing complex TORC2 complex
A, C	Serine/threonine-protein kinase TOR2	1-phosphatidylinositol 4-kinase activity phosphatidylinositol kinase activity kinase activity lipid kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups catalytic activity, acting on a protein protein kinase activity protein serine kinase activity binding adenyl ribonucleotide binding nucleotide binding 1-phosphatidylinositol 4-kinase activity phosphatidylinositol kinase activity kinase activity lipid kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups catalytic activity, acting on a protein protein kinase activity protein serine kinase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity protein-containing complex binding	snRNA modification regulation of cellular process RNA metabolic process regulation of snRNA pseudouridine synthesis regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA metabolic process snRNA metabolic process snRNA processing RNA processing regulation of nucleobase-containing compound metabolic process pseudouridine synthesis snRNA modification regulation of cellular process RNA metabolic process regulation of snRNA pseudouridine synthesis regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA metabolic process snRNA metabolic process snRNA processing RNA processing regulation of nucleobase-containing compound metabolic process pseudouridine synthesis regulation of biological process snRNA pseudouridine synthesis biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA modification biosynthetic process macromolecule modification metabolic process cellular process macromolecule metabolic process regulation of metabolic process cellular response to stimulus response to nutrient levels cellular response to nitrogen levels response to stimulus cellular response to starvation cellular response to nutrient levels cellular response to stress cellular response to nitrogen starvation response to stress response to starvation cellular component organization establishment or maintenance of actin cytoskeleton polarity organelle organization establishment or maintenance of cytoskeleton polarity actin cytoskeleton organization actin filament-based process cellular component organization or biogenesis establishment or maintenance of cell polarity cytoskeleton organization cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis positive regulation of cell communication small GTPase-mediated signal transduction positive regulation of signal transduction signaling regulation of small GTPase mediated signal transduction positive regulation of biological process regulation of signal transduction intracellular signal transduction Rho protein signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of signaling positive regulation of intracellular signal transduction regulation of Rho protein signal transduction positive regulation of Rho protein signal transduction regulation of response to stimulus regulation of cell communication positive regulation of small GTPase mediated signal transduction positive regulation of signaling regulation of growth regulation of cellular component organization growth regulation of cell growth cell growth TOR signaling TORC1 signaling negative regulation of catabolic process catabolic process macroautophagy negative regulation of metabolic process autophagy negative regulation of biological process regulation of catabolic process regulation of autophagy negative regulation of macroautophagy regulation of macroautophagy negative regulation of autophagy negative regulation of cellular process process utilizing autophagic mechanism cell cycle regulation of cell cycle response to chemical response to nutrient regulation of localization import into cell positive regulation of cellular component organization regulation of transport transport regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport localization positive regulation of endocytosis positive regulation of transport endocytosis regulation of endocytosis	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell periphery plasma membrane membrane protein-containing complex TOR complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell periphery plasma membrane membrane protein-containing complex TOR complex intracellular protein-containing complex TORC2 complex vacuolar membrane storage vacuole lytic vacuole vacuole fungal-type vacuole lytic vacuole membrane bounding membrane of organelle organelle membrane fungal-type vacuole membrane TORC1 complex nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I, J	IPR031313	SAPK-interacting protein 1, Pleckstrin-homology domain	Domain
I, J	IPR011993	PH-like domain superfamily	Homologous Superfamily
I, J	IPR031567	Sin1, middle CRIM domain	Domain
I, J	IPR056385	AVO1/Sin1, ubiquitin-like domain	Domain
I, J	IPR008828	TORC2 component Sin1/Avo1	Family
G, H	IPR002110	Ankyrin repeat	Repeat
G, H	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
B, D	IPR019775	WD40 repeat, conserved site	Conserved Site
B, D	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
B, D	IPR020472	PAC1/LIS1-like, WD-40 repeat	Repeat
B, D	IPR001680	WD40 repeat	Repeat
B, D	IPR037588	Target of rapamycin complex subunit LST8	Family
B, D	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, C	IPR026683	Serine/threonine-protein kinase TOR, catalytic domain	Domain
A, C	IPR016024	Armadillo-type fold	Homologous Superfamily
A, C	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
A, C	IPR003152	FATC domain	Domain
A, C	IPR024585	Serine/threonine-protein kinase mTOR domain	Domain
A, C	IPR011989	Armadillo-like helical	Homologous Superfamily
A, C	IPR009076	FKBP12-rapamycin binding domain	Domain
A, C	IPR000403	Phosphatidylinositol 3-/4-kinase, catalytic domain	Domain
A, C	IPR050517	DNA Damage Response and Repair Kinase	Family
A, C	IPR003151	PIK-related kinase, FAT	Domain
A, C	IPR018936	Phosphatidylinositol 3-/4-kinase, conserved site	Conserved Site
A, C	IPR036940	Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily	Homologous Superfamily
A, C	IPR057564	Serine/threonine-protein kinase ATR-like, HEAT repeats	Domain
A, C	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, C	IPR036738	FKBP12-rapamycin binding domain superfamily	Homologous Superfamily
A, C	IPR014009	PIK-related kinase, FAT domain	Domain