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- PDB-9zbk: mTORC2 in complex with Akt1 -

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Basic information

Entry
Database: PDB / ID: 9zbk
TitlemTORC2 in complex with Akt1
Components
  • (Target of rapamycin complex ...) x 2
  • RAC-alpha serine/threonine-protein kinase
  • Rapamycin-insensitive companion of mTOR
  • Serine/threonine-protein kinase mTOR
KeywordsTRANSFERASE / cellular growth control / Torin
Function / homology
Function and homology information


positive regulation of endodeoxyribonuclease activity / regulation of tRNA methylation / negative regulation of protein maturation / negative regulation of fatty acid beta-oxidation / positive regulation of protein localization to endoplasmic reticulum / regulation of glycogen biosynthetic process / negative regulation of lymphocyte migration / negative regulation of protein localization to lysosome / cellular response to decreased oxygen levels / cellular response to rapamycin ...positive regulation of endodeoxyribonuclease activity / regulation of tRNA methylation / negative regulation of protein maturation / negative regulation of fatty acid beta-oxidation / positive regulation of protein localization to endoplasmic reticulum / regulation of glycogen biosynthetic process / negative regulation of lymphocyte migration / negative regulation of protein localization to lysosome / cellular response to decreased oxygen levels / cellular response to rapamycin / maintenance of protein location in mitochondrion / mammalian oogenesis stage / AKT-mediated inactivation of FOXO1A / negative regulation of long-chain fatty acid import across plasma membrane / Negative regulation of the PI3K/AKT network / regulation of type B pancreatic cell development / maternal placenta development / positive regulation of anaphase-promoting complex-dependent catabolic process / : / potassium channel activator activity / AKT phosphorylates targets in the nucleus / positive regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process / RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / activation-induced cell death of T cells / T-helper 1 cell lineage commitment / 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 / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of cilium assembly / regulation of membrane permeability / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / TORC2 complex / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / heart valve morphogenesis / negative regulation of lysosome organization / positive regulation of TORC2 signaling / positive regulation of glucose metabolic process / voluntary musculoskeletal movement / TORC1 complex / RUNX2 regulates genes involved in cell migration / beta-arrestin-dependent dopamine receptor signaling pathway / cellular response to peptide / regulation of cellular response to oxidative stress / calcineurin-NFAT signaling cascade / positive regulation of organ growth / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / regulation of osteoclast differentiation / mammary gland epithelial cell differentiation / fibroblast migration / interleukin-18-mediated signaling pathway / positive regulation of sodium ion transport / MTOR signalling / response to growth factor / energy reserve metabolic process / regulation of lysosome organization / cellular response to L-leucine / regulation of autophagosome assembly / Energy dependent regulation of mTOR by LKB1-AMPK / cellular response to nutrient / response to fluid shear stress / RAB GEFs exchange GTP for GDP on RABs / Amino acids regulate mTORC1 / cellular response to granulocyte macrophage colony-stimulating factor stimulus / negative regulation of leukocyte cell-cell adhesion / phosphatidic acid binding / negative regulation of Ras protein signal transduction / glycogen biosynthetic process / peripheral nervous system myelin maintenance / cell migration involved in sprouting angiogenesis / cellular response to methionine / embryo development ending in birth or egg hatching / phosphatidylinositol-3,4-bisphosphate binding / positive regulation of protein localization to cell surface / negative regulation of cell size / complement receptor mediated signaling pathway / phosphorylation / TORC2 signaling / sphingosine-1-phosphate receptor signaling pathway / cellular response to osmotic stress / phosphatidylinositol-3,5-bisphosphate binding / AKT phosphorylates targets in the cytosol / cell projection organization / regulation of postsynapse organization / anoikis / inositol hexakisphosphate binding / positive regulation of fibroblast migration / response to growth hormone / cardiac muscle cell development / labyrinthine layer blood vessel development / negative regulation of calcineurin-NFAT signaling cascade / positive regulation of ubiquitin-dependent protein catabolic process / execution phase of apoptosis
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 / Protein kinase B alpha, catalytic 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 / Protein Kinase B, pleckstrin homology domain / 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 / Protein kinase, C-terminal / Protein kinase C terminal domain / : / 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. / Extension to Ser/Thr-type protein kinases / 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 / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Trp-Asp (WD) repeats signature. / Protein kinase domain / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / RAC-alpha serine/threonine-protein kinase / 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: 2.6 Å
AuthorsWranik, M. / Lee, J.M. / Rogala, K.B.
Funding support United States, Germany, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R00 CA255926 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 GM150935 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA124435 United States
Other privateShmunis Family Innovation Award United States
Other privateBridging Excellence Fellowship Germany
Other private United States
CitationJournal: Science / Year: 2026
Title: Structural basis for the recruitment and selective phosphorylation of Akt by mTORC2.
Authors: Martin S Taylor / Maggie Chen / Matthew Hancock / Maximilian Wranik / Bryant D Miller / Timothy R O'Meara / Brad A Palanski / Scott B Ficarro / Brian J Groendyke / Yufei Xiang / Kazuma T ...Authors: Martin S Taylor / Maggie Chen / Matthew Hancock / Maximilian Wranik / Bryant D Miller / Timothy R O'Meara / Brad A Palanski / Scott B Ficarro / Brian J Groendyke / Yufei Xiang / Kazuma T Kondo / Karen Y Linde-Garelli / Michelle J Lee / Dibyendu Mondal / Daniel Freund / Samantha Congreve / Kaay Matas / Maximiliaan Hennink / Kera Xibinaku / Max L Valenstein / Trevor van Eeuwen / Jarrod A Marto / Andrej Sali / Yi Shi / Nathanael S Gray / David M Sabatini / Nam Chu / Kacper B Rogala / Philip A Cole /
Abstract: The mechanistic target of rapamycin (mTOR) protein kinase forms two multiprotein complexes, mTORC1 and mTORC2, that function in distinct signaling pathways. mTORC1 is regulated by nutrients, and ...The mechanistic target of rapamycin (mTOR) protein kinase forms two multiprotein complexes, mTORC1 and mTORC2, that function in distinct signaling pathways. mTORC1 is regulated by nutrients, and mTORC2 is a central node in phosphoinositide-3 kinase (PI3K) and small guanosine triphosphate Ras signaling networks commonly deregulated in cancer and diabetes. Although mTOR phosphorylates many substrates in vitro, in cells, mTORC1 and mTORC2 have high specificity: mTORC2 phosphorylates the protein kinases Akt and PKC, but not closely related kinases that are mTORC1 substrates. To understand how mTORC2 recognizes substrates, we created semisynthetic probes to trap the mTORC2 :: Akt complex and determine its structure. Whereas most protein kinases recognize amino acids adjacent to the phosphorylation site, local sequence contributes little to substrate recognition by mTORC2. Instead, the specificity determinants were secondary and tertiary structural elements of Akt that bound the mTORC2 component mSin1 distal to the mTOR active site and were conserved among at least 18 related substrates. These results reveal how mTORC2 recognizes its canonical substrates and may enable the design of mTORC2-specific inhibitors.
History
DepositionNov 20, 2025Deposition site: RCSB / Processing site: RCSB
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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: Target of rapamycin complex subunit LST8
C: Rapamycin-insensitive companion of mTOR
D: Target of rapamycin complex 2 subunit MAPKAP1
E: RAC-alpha serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)574,4167
Polymers573,7455
Non-polymers6712
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-1), (-1), (1)333.965, 333.965

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Components

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Protein , 3 types, 3 molecules ACE

#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: 280530.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTOR, FRAP, FRAP1, FRAP2, RAFT1, RAPT1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
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: 188389.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RICTOR, KIAA1999 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6R327
#5: Protein RAC-alpha serine/threonine-protein kinase / Protein kinase B / PKB / Protein kinase B alpha / PKB alpha / Proto-oncogene c-Akt / RAC-PK-alpha


Mass: 39206.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence position 333 contains the chemically modification T1C (C-T1C)
Source: (gene. exp.) Homo sapiens (human) / Gene: AKT1, PKB, RAC / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P31749, non-specific serine/threonine protein kinase

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Target of rapamycin complex ... , 2 types, 2 molecules BD

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


Mass: 35152.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLST8, GBL, LST8 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / 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: 30466.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAP1, MIP1, SIN1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BPZ7

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Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-A1AID / (1M,9M)-1-{4-[4-(prop-2-enoyl)piperazin-1-yl]-3-(trifluoromethyl)phenyl}-9-(quinolin-3-yl)benzo[h][1,6]naphthyridin-2(1H)-one / Protein kinase B / PKB / Protein kinase B alpha / PKB alpha / Proto-oncogene c-Akt / RAC-PK-alpha


Mass: 605.608 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C35H26F3N5O2
Details: Sequence position 333 contains the chemically modification T1C (C-T1C)
Source: (gene. exp.) Homo sapiens (human) / Gene: AKT1, PKB, RAC / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / Feature type: SUBJECT OF INVESTIGATION / References: non-specific serine/threonine protein kinase

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Details

Has ligand of interestY
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: mTORC2 in complex with Akt1 / Type: COMPLEX / Entity ID: #1, #3-#4, #2, #5 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf9
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 4D-STEM / Nominal defocus max: 2100 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Image recordingElectron dose: 69.72 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topaz2.6.4particle selection
2PHENIX1.21.1_5286model refinement
13cryoSPARC53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3169869 / Symmetry type: POINT
RefinementHighest resolution: 2.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00231174
ELECTRON MICROSCOPYf_angle_d0.4842422
ELECTRON MICROSCOPYf_dihedral_angle_d10.53210841
ELECTRON MICROSCOPYf_chiral_restr0.0384975
ELECTRON MICROSCOPYf_plane_restr0.0045492

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