[English] 日本語
Yorodumi
- PDB-6zwm: cryo-EM structure of human mTOR complex 2, overall refinement -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zwm
Titlecryo-EM structure of human mTOR complex 2, overall refinement
Components
  • (Target of rapamycin complex ...MTOR) x 2
  • Rapamycin-insensitive companion of mTOR
  • Serine/threonine-protein kinase mTOR
KeywordsTRANSFERASE / mTOR / Kinase / Complex / Inositol
Function / homology
Function and homology information


TORC2 signaling / regulation of peptidyl-serine phosphorylation / establishment or maintenance of actin cytoskeleton polarity / positive regulation of skeletal muscle hypertrophy / negative regulation of iodide transmembrane transport / positive regulation of cytoplasmic translational initiation / positive regulation of granulosa cell proliferation / positive regulation of wound healing, spreading of epidermal cells / negative regulation of muscle atrophy / negative regulation of cholangiocyte apoptotic process ...TORC2 signaling / regulation of peptidyl-serine phosphorylation / establishment or maintenance of actin cytoskeleton polarity / positive regulation of skeletal muscle hypertrophy / negative regulation of iodide transmembrane transport / positive regulation of cytoplasmic translational initiation / positive regulation of granulosa cell proliferation / positive regulation of wound healing, spreading of epidermal cells / negative regulation of muscle atrophy / negative regulation of cholangiocyte apoptotic process / regulation of cellular response to oxidative stress / regulation of fatty acid beta-oxidation / RNA polymerase III type 1 promoter sequence-specific DNA binding / RNA polymerase III type 2 promoter sequence-specific DNA binding / positive regulation of cholangiocyte proliferation / positive regulation of eating behavior / regulation of locomotor rhythm / regulation of carbohydrate utilization / nucleus localization / cardiac muscle cell development / regulation of response to food / cellular response to leucine starvation / cellular response to leucine / TFIIIC-class transcription factor complex binding / positive regulation of sensory perception of pain / heart valve morphogenesis / small GTPase binding => GO:0031267 / phosphatidic acid binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / regulation of membrane permeability / regulation of brown fat cell differentiation / TORC1 complex / TORC1 signaling / TORC2 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / voluntary musculoskeletal movement / regulation of protein kinase B signaling / regulation of osteoclast differentiation / regulation of glycogen biosynthetic process / energy reserve metabolic process / positive regulation of keratinocyte migration / positive regulation of neuron maturation / regulation of phosphorylation / positive regulation of transcription by RNA polymerase III / negative regulation of cell size / ruffle organization / embryo development ending in birth or egg hatching / lysosome organization / negative regulation of Ras protein signal transduction / anoikis / positive regulation of TOR signaling / cellular response to nutrient levels / phosphatidylinositol-3,5-bisphosphate binding / mRNA stabilization / positive regulation of glial cell proliferation / phosphatidylinositol-3,4-bisphosphate binding / positive regulation of cell growth involved in cardiac muscle cell development / regulation of establishment of cell polarity / regulation of myelination / positive regulation of dendritic spine development / positive regulation of lamellipodium assembly / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of macroautophagy / postsynaptic cytosol / spinal cord development / regulation of cell size / germ cell development / enzyme activator activity / maternal process involved in female pregnancy / TOR signaling / positive regulation of myotube differentiation / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of actin filament polymerization / positive regulation of epithelial to mesenchymal transition / social behavior / positive regulation of lipid biosynthetic process / cardiac muscle contraction / protein catabolic process / positive regulation of oligodendrocyte differentiation / long-term memory / response to morphine / positive regulation of phosphoprotein phosphatase activity / heart morphogenesis / regulation of macroautophagy / endomembrane system / regulation of GTPase activity / cellular response to amino acid starvation / regulation of actin cytoskeleton organization / substantia nigra development / positive regulation of stress fiber assembly / response to insulin / response to cocaine / 'de novo' pyrimidine nucleobase biosynthetic process / response to amino acid / cell aging / negative regulation of protein ubiquitination / phagocytic vesicle / actin cytoskeleton reorganization / phosphorylation / establishment of cell polarity
Protein kinase-like domain superfamily / PIK-related kinase / Rapamycin-insensitive companion of mTOR, phosphorylation-site / Pianissimo family / Rapamycin-insensitive companion of mTOR, N-terminal domain / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Rapamycin-insensitive companion of mTOR, domain 4 ...Protein kinase-like domain superfamily / PIK-related kinase / Rapamycin-insensitive companion of mTOR, phosphorylation-site / Pianissimo family / Rapamycin-insensitive companion of mTOR, N-terminal domain / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Rapamycin-insensitive companion of mTOR, domain 4 / Quinoprotein alcohol dehydrogenase-like superfamily / Armadillo-type fold / WD40-repeat-containing domain / Phosphatidylinositol 3/4-kinase, conserved site / WD40 repeat, conserved site / Serine/threonine-protein kinase TOR / G-protein beta WD-40 repeat / Rapamycin-insensitive companion of mTOR, domain 5 / Rapamycin-insensitive companion of mTOR, middle domain / SAPK-interacting protein 1, Pleckstrin-homology domain / Sin1, N-terminal / FKBP12-rapamycin binding domain / FATC domain / PIK-related kinase, FAT / WD40 repeat / Target of rapamycin complex subunit LST8 / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / FKBP12-rapamycin binding domain superfamily / Domain of unknown function DUF3385, target of rapamycin protein / Sin1, middle CRIM domain
Serine/threonine-protein kinase mTOR / Rapamycin-insensitive companion of mTOR / Target of rapamycin complex 2 subunit MAPKAP1 / Target of rapamycin complex subunit LST8
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsScaiola, A. / Mangia, F. / Imseng, S. / Boehringer, D. / Ban, N. / Maier, T.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation179323 Switzerland
Swiss National Science Foundation177084 Switzerland
Swiss National Science Foundation138262
CitationJournal: Sci Adv / Year: 2020
Title: The 3.2-Å resolution structure of human mTORC2.
Authors: Alain Scaiola / Francesca Mangia / Stefan Imseng / Daniel Boehringer / Karolin Berneiser / Mitsugu Shimobayashi / Edward Stuttfeld / Michael N Hall / Nenad Ban / Timm Maier /
Abstract: The protein kinase mammalian target of rapamycin (mTOR) is the central regulator of cell growth. Aberrant mTOR signaling is linked to cancer, diabetes, and neurological disorders. mTOR exerts its ...The protein kinase mammalian target of rapamycin (mTOR) is the central regulator of cell growth. Aberrant mTOR signaling is linked to cancer, diabetes, and neurological disorders. mTOR exerts its functions in two distinct multiprotein complexes, mTORC1 and mTORC2. Here, we report a 3.2-Å resolution cryo-EM reconstruction of mTORC2. It reveals entangled folds of the defining Rictor and the substrate-binding SIN1 subunits, identifies the carboxyl-terminal domain of Rictor as the source of the rapamycin insensitivity of mTORC2, and resolves mechanisms for mTORC2 regulation by complex destabilization. Two previously uncharacterized small-molecule binding sites are visualized, an inositol hexakisphosphate (InsP6) pocket in mTOR and an mTORC2-specific nucleotide binding site in Rictor, which also forms a zinc finger. Structural and biochemical analyses suggest that InsP6 and nucleotide binding do not control mTORC2 activity directly but rather have roles in folding or ternary interactions. These insights provide a firm basis for studying mTORC2 signaling and for developing mTORC2-specific inhibitors.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-11488
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)1,157,32718
Polymers1,153,6958
Non-polymers3,63210
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area44160 Å2
ΔGint-206 kcal/mol
Surface area320140 Å2
MethodPISA

-
Components

-
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


Mass: 289257.969 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: Spodoptera frugiperda (fall armyworm)
References: UniProt: P42345, non-specific serine/threonine protein kinase
#3: Protein Rapamycin-insensitive companion of mTOR / AVO3 homolog / hAVO3


Mass: 192472.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RICTOR, KIAA1999 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6R327

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

#2: Protein Target of rapamycin complex subunit LST8 / MTOR / 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: 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 / mSIN1


Mass: 59206.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MAFLDNPTIILAHIRQSHVTSDDTGMCEMVLIDHDVDLEKIHPPSMPGDSGSEIQGSNGE TQGYVYAQSVDITSSWDFGIRRRSNTAQRLERLRKERQNQIKCKNIQWKERNSKQSAQEL KSLFEKKSLKEKPPISGKQSILSVRLEQCPLQLNNPFNEYSKFDGKGHVGTTATKKIDVY ...Details: MAFLDNPTIILAHIRQSHVTSDDTGMCEMVLIDHDVDLEKIHPPSMPGDSGSEIQGSNGE TQGYVYAQSVDITSSWDFGIRRRSNTAQRLERLRKERQNQIKCKNIQWKERNSKQSAQEL KSLFEKKSLKEKPPISGKQSILSVRLEQCPLQLNNPFNEYSKFDGKGHVGTTATKKIDVY LPLHSSQDRLLPMTVVTMASARVQDLIGLICWQYTSEGREPKLNDNVSAYCLHIAEDDGE VDTDFPPLDSNEPIHKFGFSTLALVEKYSSPGLTSKESLFVRINAAHGFSLIQVDNTKVT MKEILLKAVKRRKGSQKVSGPQYRLEKQSEPNVAVDLDSTLESQSAWEFCLVRENSSRAD GVFEEDSQIDIATVQDMLSSHHYKSFKVSMIHRLRFTTDVQLGISGDKVEIDPVTNQKAS TKFWIKQKPISIDSDLLCACDLAEEKSPSHAIFKLTYLSNHDYKHLYFESDAATVNEIVL KVNYILESRASTARADYFAQKQRKLNRRTSFSFQKEKKSGQQ
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAP1, MIP1, SIN1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BPZ7

-
Non-polymers , 4 types, 10 molecules

#5: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-ACE / ACETYL GROUP / Acetyl group


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: human mTOR complex 2MTORC2 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 1.15 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8.5
SpecimenConc.: 0.37 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / C2 aperture diameter: 100 µm
Image recordingElectron dose: 70 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM softwareName: EPU / Version: 2 / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 293038 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more