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- PDB-9tds: cryo-EM structure of dephosphorylated mTOR complex 2, overall ref... -

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Basic information

Entry
Database: PDB / ID: 9tds
Titlecryo-EM structure of dephosphorylated mTOR complex 2, overall refinement
Components
  • (Target of rapamycin complex ...) x 2
  • Rapamycin-insensitive companion of mTOR
  • Serine/threonine-protein kinase mTOR
KeywordsTRANSFERASE / Kinase / Complex / Signaling protein
Function / homology
Function and homology information


cardiac cell development / positive regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process / RNA polymerase III type 2 promoter sequence-specific DNA binding / T-helper 1 cell lineage commitment / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction ...cardiac cell development / positive regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process / RNA polymerase III type 2 promoter sequence-specific DNA binding / T-helper 1 cell lineage commitment / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / TORC2 complex / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / regulation of lysosome organization / TORC1 complex / regulation of cellular response to oxidative stress / negative regulation of lysosome organization / regulation of osteoclast differentiation / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / positive regulation of keratinocyte migration / MTOR signalling / cellular response to L-leucine / Energy dependent regulation of mTOR by LKB1-AMPK / cellular response to nutrient / regulation of autophagosome assembly / Amino acids regulate mTORC1 / negative regulation of Ras protein signal transduction / Dengue virus modulates apoptosis / embryo development ending in birth or egg hatching / phosphatidic acid binding / cellular response to methionine / phosphatidylinositol-3,4-bisphosphate binding / TORC2 signaling / cellular response to osmotic stress / phosphatidylinositol-3,5-bisphosphate binding / anoikis / inositol hexakisphosphate binding / negative regulation of protein localization to nucleus / positive regulation of ubiquitin-dependent protein catabolic process / negative regulation of macroautophagy / regulation of cell size / lipid biosynthetic process / Macroautophagy / Constitutive Signaling by AKT1 E17K in Cancer / positive regulation of transcription by RNA polymerase III / TORC1 signaling / positive regulation of protein kinase activity / behavioral response to pain / phosphatidylinositol-3,4,5-trisphosphate binding / response to amino acid / TOR signaling / mTORC1-mediated signalling / CD28 dependent PI3K/Akt signaling / HSF1-dependent transactivation / positive regulation of TOR signaling / positive regulation of translational initiation / positive regulation of lipid biosynthetic process / enzyme-substrate adaptor activity / positive regulation of epithelial to mesenchymal transition / T cell costimulation / neuronal action potential / vascular endothelial cell response to laminar fluid shear stress / regulation of cellular response to heat / regulation of macroautophagy / 'de novo' pyrimidine nucleobase biosynthetic process / cytoskeleton organization / phagocytic vesicle / positive regulation of endothelial cell proliferation / phosphatidylinositol-4,5-bisphosphate binding / negative regulation of insulin receptor signaling pathway / endomembrane system / substantia nigra development / cellular response to nutrient levels / positive regulation of glycolytic process / negative regulation of autophagy / regulation of signal transduction by p53 class mediator / cellular response to amino acid starvation / cellular response to starvation / Regulation of PTEN gene transcription / cellular response to amino acid stimulus / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of translation / regulation of actin cytoskeleton organization / TP53 Regulates Metabolic Genes / non-specific protein-tyrosine kinase / regulation of cell growth / non-membrane spanning protein tyrosine kinase activity / phosphoprotein binding / response to nutrient levels / PML body / regulation of circadian rhythm / small GTPase binding / cellular response to insulin stimulus / Regulation of TP53 Degradation / late endosome / nuclear envelope / PIP3 activates AKT signaling
Similarity search - Function
Rapamycin-insensitive companion of mTOR, phosphorylation-site / Rapamycin-insensitive companion of mTOR, phosphorylation-site / Rapamycin-insensitive companion of mTOR, phosphorylation-site / Rapamycin-insensitive companion of mTOR, N-terminal domain / Pianissimo family / Rapamycin-insensitive companion of mTOR, middle domain / Rapamycin-insensitive companion of mTOR, domain 5 / Rapamycin-insensitive companion of mTOR, domain 4 / Rapamycin-insensitive companion of mTOR RasGEF_N domain / Rapamycin-insensitive companion of mTOR, N-term ...Rapamycin-insensitive companion of mTOR, phosphorylation-site / Rapamycin-insensitive companion of mTOR, phosphorylation-site / Rapamycin-insensitive companion of mTOR, phosphorylation-site / Rapamycin-insensitive companion of mTOR, N-terminal domain / Pianissimo family / Rapamycin-insensitive companion of mTOR, middle domain / Rapamycin-insensitive companion of mTOR, domain 5 / Rapamycin-insensitive companion of mTOR, domain 4 / Rapamycin-insensitive companion of mTOR RasGEF_N domain / Rapamycin-insensitive companion of mTOR, N-term / Rapamycin-insensitive companion of mTOR, middle domain / Rapamycin-insensitive companion of mTOR, domain 5 / Rapamycin-insensitive companion of mTOR RasGEF_N domain / Rapamycin-insensitive companion of mTOR, middle domain / Rapamycin-insensitive companion of mTOR, N-term / Rapamycin-insensitive companion of mTOR, domain 5 / : / SIN1 Ras-binding domain / Sin1, N-terminal / Stress-activated map kinase interacting protein 1 (SIN1) / TORC2 component Sin1/Avo1 / SAPK-interacting protein 1, Pleckstrin-homology domain / Sin1, middle CRIM domain / SAPK-interacting protein 1 (Sin1), middle CRIM domain / SAPK-interacting protein 1 (Sin1), Pleckstrin-homology / Target of rapamycin complex subunit LST8 / Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / Rapamycin binding domain / : / Serine/threonine-protein kinase ATR-like, HEAT repeats / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Quinoprotein alcohol dehydrogenase-like superfamily / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Armadillo-like helical / PH-like domain superfamily / Tetratricopeptide-like helical domain superfamily / WD domain, G-beta repeat / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Serine/threonine-protein kinase mTOR / Rapamycin-insensitive companion of mTOR / Target of rapamycin complex 2 subunit MAPKAP1 / Target of rapamycin complex subunit LST8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHay, I.M. / Anandapadamanaban, M. / Williams, R.L.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Biorxiv / Year: 2026
Title: Structural basis for a phosphoinositide-driven mTORC2-AKT positive feedback loop
Authors: Hay, I.M. / Bourguet, M. / Ahsan, B. / Perisic, O. / Anandapadamanaban, M. / Williams, R.L.
History
DepositionNov 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase mTOR
B: Serine/threonine-protein kinase mTOR
C: Target of rapamycin complex subunit LST8
D: Target of rapamycin complex subunit LST8
E: Rapamycin-insensitive companion of mTOR
F: Rapamycin-insensitive companion of mTOR
G: Target of rapamycin complex 2 subunit MAPKAP1
H: Target of rapamycin complex 2 subunit MAPKAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,169,69412
Polymers1,168,2438
Non-polymers1,4514
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 4 molecules ABEF

#1: Protein Serine/threonine-protein kinase mTOR / FK506-binding protein 12-rapamycin complex-associated protein 1 / FKBP12-rapamycin complex- ...FK506-binding protein 12-rapamycin complex-associated protein 1 / FKBP12-rapamycin complex-associated protein / Mammalian target of rapamycin / mTOR / Mechanistic target of rapamycin / Rapamycin and FKBP12 target 1 / Rapamycin target protein 1 / Tyrosine-protein kinase mTOR


Mass: 293557.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTOR, FRAP, FRAP1, FRAP2, RAFT1, RAPT1 / Production host: Homo sapiens (human)
References: UniProt: P42345, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase
#3: Protein Rapamycin-insensitive companion of mTOR / AVO3 homolog / hAVO3


Mass: 195552.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RICTOR, KIAA1999 / Production host: Homo sapiens (human) / References: UniProt: Q6R327

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Target of rapamycin complex ... , 2 types, 4 molecules CDGH

#2: Protein Target of rapamycin complex subunit LST8 / TORC subunit LST8 / G protein beta subunit-like / Protein GbetaL / Mammalian lethal with SEC13 ...TORC subunit LST8 / G protein beta subunit-like / Protein GbetaL / Mammalian lethal with SEC13 protein 8 / mLST8


Mass: 35910.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLST8, GBL, LST8 / Production host: Homo sapiens (human) / References: UniProt: Q9BVC4
#4: Protein Target of rapamycin complex 2 subunit MAPKAP1 / TORC2 subunit MAPKAP1 / Mitogen-activated protein kinase 2-associated protein 1 / Stress-activated ...TORC2 subunit MAPKAP1 / Mitogen-activated protein kinase 2-associated protein 1 / Stress-activated map kinase-interacting protein 1 / SAPK-interacting protein 1 / mSIN1


Mass: 59101.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAP1, MIP1, SIN1 / Production host: Homo sapiens (human) / References: UniProt: Q9BPZ7

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Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: mTOR complex 2, dephosphorylated / Type: COMPLEX
Details: mTOR complex 2 dephosphorylated in vitro with lambda protein phosphatase
Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.58 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
120 mMHEPES1
2250 mMNaCl1
31 mMTCEP1
SpecimenConc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 287 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
4RELION5CTF correction
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 191304 / Symmetry type: POINT

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