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- PDB-5zcs: 4.9 Angstrom Cryo-EM structure of human mTOR complex 2 -

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Entry
Database: PDB / ID: 5zcs
Title4.9 Angstrom Cryo-EM structure of human mTOR complex 2
Components
  • Rapamycin-insensitive companion of mTOR
  • Serine/threonine-protein kinase mTOR
  • Target of rapamycin complex 2 subunit MAPKAP1
  • Target of rapamycin complex subunit LST8MTOR
KeywordsGENE REGULATION / Cryo-EM structure human mTORC2
Function / homologyRapamycin-insensitive companion of mTOR, phosphorylation-site / WD40/YVTN repeat-like-containing domain superfamily / SAPK-interacting protein 1, Pleckstrin-homology domain / Rapamycin-insensitive companion of mTOR, domain 5 / Rapamycin-insensitive companion of mTOR, middle domain / Rapamycin-insensitive companion of mTOR, phosphorylation-site / Pianissimo family / Rapamycin-insensitive companion of mTOR, N-terminal domain / Serine/threonine-protein kinase TOR / Domain of unknown function DUF3385, target of rapamycin protein ...Rapamycin-insensitive companion of mTOR, phosphorylation-site / WD40/YVTN repeat-like-containing domain superfamily / SAPK-interacting protein 1, Pleckstrin-homology domain / Rapamycin-insensitive companion of mTOR, domain 5 / Rapamycin-insensitive companion of mTOR, middle domain / Rapamycin-insensitive companion of mTOR, phosphorylation-site / Pianissimo family / Rapamycin-insensitive companion of mTOR, N-terminal domain / Serine/threonine-protein kinase TOR / Domain of unknown function DUF3385, target of rapamycin protein / G-protein beta WD-40 repeat / WD40 repeat, conserved site / FAT domain profile. / Phosphatidylinositol 3/4-kinase, conserved site / WD40-repeat-containing domain / Armadillo-type fold / Trp-Asp (WD) repeats circular profile. / Sin1, N-terminal / PIK-related kinase / PH-like domain superfamily / Tetratricopeptide-like helical domain superfamily / Armadillo-like helical / Quinoprotein alcohol dehydrogenase-like superfamily / Protein kinase-like domain superfamily / FKBP12-rapamycin binding domain / Phosphatidylinositol 3- and 4-kinases family profile. / Trp-Asp (WD) repeats profile. / FATC domain / PIK-related kinase, FAT / WD40 repeat / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinases signature 2. / Sin1, middle CRIM domain / Rapamycin-insensitive companion of mTOR, domain 4 / FKBP12-rapamycin binding domain superfamily / FATC domain / SAPK-interacting protein 1 (Sin1), Pleckstrin-homology / SAPK-interacting protein 1 (Sin1), middle CRIM domain / Trp-Asp (WD) repeats signature. / Rapamycin-insensitive companion of mTOR, N-term / Rapamycin-insensitive companion of mTOR RasGEF_N domain / Regulation of PTEN gene transcription / Domain of unknown function (DUF3385) / Phosphatidylinositol 3- and 4-kinases signature 1. / FKBP12-rapamycin binding domain / Rapamycin-insensitive companion of mTOR, middle domain / Regulation of TP53 Degradation / Constitutive Signaling by AKT1 E17K in Cancer / TP53 Regulates Metabolic Genes / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Stress-activated map kinase interacting protein 1 (SIN1) / VEGFR2 mediated vascular permeability / mTORC1-mediated signalling / FATC domain profile. / PIP3 activates AKT signaling / Target of rapamycin complex subunit LST8 / Macroautophagy / mTOR signalling / Rapamycin-insensitive companion of mTOR, domain 5 / HSF1-dependent transactivation / Phosphatidylinositol 3- and 4-kinase / FAT domain / Energy dependent regulation of mTOR by LKB1-AMPK / WD domain, G-beta repeat / CD28 dependent PI3K/Akt signaling / TORC2 signaling / regulation of protein kinase B 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 / negative regulation of cholangiocyte apoptotic process / positive regulation of cholangiocyte proliferation / positive regulation of wound healing, spreading of epidermal cells / regulation of fatty acid beta-oxidation / positive regulation of granulosa cell proliferation / negative regulation of muscle atrophy / RNA polymerase III type 1 promoter DNA binding / RNA polymerase III type 2 promoter DNA binding / positive regulation of eating behavior / RNA polymerase III type 3 promoter DNA binding / cellular response to leucine starvation / T-helper 1 cell lineage commitment / phosphatidic acid binding / cardiac muscle cell development / regulation of carbohydrate utilization / regulation of response to food / TFIIIC-class transcription factor binding / cellular response to leucine / Ras GTPase binding / TORC1 complex / heart valve morphogenesis / TORC1 signaling / TORC2 complex / positive regulation of sensory perception of pain / regulation of membrane permeability / positive regulation of keratinocyte migration / regulation of brown fat cell differentiation / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.9 Å resolution
AuthorsChen, X. / Liu, M. / Tian, Y. / Wang, H. / Wang, J. / Xu, Y.
CitationJournal: Cell Res. / Year: 2018
Title: Cryo-EM structure of human mTOR complex 2.
Authors: Xizi Chen / Mengjie Liu / Yuan Tian / Jiabei Li / Yilun Qi / Dan Zhao / Zihan Wu / Min Huang / Catherine C L Wong / Hong-Wei Wang / Jiawei Wang / Huirong Yang / Yanhui Xu
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 20, 2018 / Release: Mar 21, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 21, 2018Structure modelrepositoryInitial release
1.1Apr 4, 2018Structure modelData collection / Database referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
1.2May 30, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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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


Theoretical massNumber of molelcules
Total (without water)1,110,9388
Polyers1,110,9388
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide Serine/threonine-protein kinase mTOR / 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: (gene. exp.) Homo sapiens (human) / Gene: MTOR, FRAP, FRAP1, FRAP2, RAFT1, RAPT1 / Cell line (production host): 293F / Production host: Homo sapiens (human)
References: UniProt: P42345, non-specific serine/threonine protein kinase
#2: Protein/peptide Target of rapamycin complex subunit LST8 / MTOR / 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: (gene. exp.) Homo sapiens (human) / Gene: MLST8, GBL, LST8 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: Q9BVC4
#3: Protein/peptide Rapamycin-insensitive companion of mTOR / AVO3 homolog / hAVO3


Mass: 175142.500 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: RICTOR, KIAA1999 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: Q6R327
#4: Protein/peptide Target of rapamycin complex 2 subunit MAPKAP1 / SIN:Stress-activated map kinase-interacting protein 1 / TORC2 subunit MAPKAP1 / Mitogen-activated protein kinase 2-associated protein 1 / Stress-activated map kinase-interacting protein 1 / mSIN1


Mass: 55158.477 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAP1, MIP1, SIN1 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: Q9BPZ7
Sequence details1. FOR ENTITY 3 (CHAINS E/F), ENTIRE SEQUENCE HAS BEEN USED IN THE EXPERIMENT. HOWEVER, C-TERMINAL ...1. FOR ENTITY 3 (CHAINS E/F), ENTIRE SEQUENCE HAS BEEN USED IN THE EXPERIMENT. HOWEVER, C-TERMINAL THREE HELIX CANNOT BE ASSIGNED ACCURATELY, AND WERE ASSIGNED TO RESIDUE NUMBER 1610-1626, 1630-1649 AND 1680-1695 TEMPORARY. THE REAL SEQUENCE FOR RESIDUE 1019-1708 SHOULD BE PSTLSLNSESTSSRHNSESESVPSSMFILEDDRFGSSSTSTFFLDINEDTEPTFYDRSGPIKDKNSFPFFASSKLVKNRILNSLTLPNKKHRSSSDPKGGKLSSESKTSNRRIRTLTEPSVDFNHSDDFTPISTVQKTLQLETS FMGNKHIEDTGSTPSIGENDLKFTKNFGTENHRENTSRERLVVESSTSSHMKIRSQSFNTDTTTSGISSMSSSPSRETVGVDATTMDTDCGSMSTVVSTKTIKTSHYLTPQSNHLSLSKSNSVSLVPPGSSHTLPRRAQSLKAP SIATIKSLADCNFSYTSSRDAFGYATLKRLQQQRMHPSLSHSEALASPAKDVLFTDTITMKANSFESRLTPSRFMKALSYASLDKEDLLSPINQNTLQRSSSVRSMVSSATYGGSDDYIGLALPVDINDIFQVKDIPYFQTKNI PPHDDRGARAFAHDAGGLPSGTGGLVKNSFHLLRQQMSLTEIMNSIHSDASLFLESTEDTGLQEHTDDNCLYCVCIEILGFQPSNQLSAICSHSDFQDIPYSDWCEQTIHNPLEVVPSKFSGISGCSDGVSQEGSASSTKSTEL LLGVKTIPDDTPMCRILLRKEVLRLVINLSSSVSTKCHETGLLTIKEKYPQTFDDICLYSEVSHLLSHCTFRLPCRRFIQELFQDVQFLQMHEEAEAVLATPPKQPIVDTSAES 2. FOR ENTITY 4 (CHAINS G/H), ENTIRE SEQUENCE HAS BEEN USED IN THE EXPERIMENT. HOWEVER, ONLY N-TERMINAL RESIDUES (SUPPOSED TO BE WITHIN RESIDUE RANGE 1-140) WERE ASSIGNED, BUT NOT ACCURATELY. THE REAL SEQUENCE FOR RESIDUE 1-140 SHOULD BE: MAFLDNPTIILAHIRQSHVTSDDTGMCEMVLIDHDVDLEKIHPPSMPGDSGSEIQGSNGETQGYVYAQSVDITSSWDFGIRRRSNTAQRLERLRKERQNQIKCKNIQWKERNSKQSAQELKSLFEKKSLKEKPPISGKQS

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: human mTOR Complex 2 / Type: COMPLEX / Entity ID: 1, 2, 3, 4 / Source: RECOMBINANT
Molecular weightValue: 1400 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Cell: 293F / Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 282 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 100 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 32 / Used frames/image: 1-32

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEM3.6image acquisition
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
10RELION2.0final Euler assignment
12RELION2.03D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C2
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 195353 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01350040
ELECTRON MICROSCOPYf_angle_d1.53268210
ELECTRON MICROSCOPYf_dihedral_angle_d7.70530230
ELECTRON MICROSCOPYf_chiral_restr0.0688168
ELECTRON MICROSCOPYf_plane_restr0.0098892

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