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- EMDB-3213: Architecture of human mTOR Complex 1 - 5.9 Angstrom reconstruction -

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Basic information

Entry
Database: EMDB / ID: EMD-3213
TitleArchitecture of human mTOR Complex 1 - 5.9 Angstrom reconstruction
Map dataHuman mTOR complex 1
Sample
  • Sample: Human mTOR complex 1
  • Protein or peptide: mTOR
  • Protein or peptide: Raptor
  • Protein or peptide: mLST8
KeywordsRapamycin / TOR / mTOR / Raptor / mLST8 / FKBP / mTORC1
Function / homology
Function and homology information


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 / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / TORC2 signaling / TORC2 complex / regulation of membrane permeability ...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 / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / TORC2 signaling / TORC2 complex / regulation of membrane permeability / cellular response to leucine starvation / negative regulation of lysosome organization / heart valve morphogenesis / TFIIIC-class transcription factor complex binding / TORC1 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / voluntary musculoskeletal movement / calcineurin-NFAT signaling cascade / positive regulation of odontoblast differentiation / regulation of osteoclast differentiation / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / regulation of lysosome organization / MTOR signalling / Amino acids regulate mTORC1 / cellular response to L-leucine / cellular response to nutrient / energy reserve metabolic process / regulation of autophagosome assembly / Energy dependent regulation of mTOR by LKB1-AMPK / TORC1 signaling / ruffle organization / serine/threonine protein kinase complex / cellular response to methionine / negative regulation of cell size / positive regulation of osteoclast differentiation / positive regulation of ubiquitin-dependent protein catabolic process / inositol hexakisphosphate binding / cellular response to osmotic stress / anoikis / negative regulation of protein localization to nucleus / cardiac muscle cell development / regulation of myelination / negative regulation of calcineurin-NFAT signaling cascade / positive regulation of transcription by RNA polymerase III / negative regulation of macroautophagy / Macroautophagy / positive regulation of myotube differentiation / regulation of cell size / positive regulation of actin filament polymerization / Constitutive Signaling by AKT1 E17K in Cancer / germ cell development / TOR signaling / behavioral response to pain / mTORC1-mediated signalling / oligodendrocyte differentiation / positive regulation of oligodendrocyte differentiation / positive regulation of translational initiation / protein kinase activator activity / social behavior / protein serine/threonine kinase inhibitor activity / CD28 dependent PI3K/Akt signaling / positive regulation of TOR signaling / HSF1-dependent transactivation / regulation of macroautophagy / enzyme-substrate adaptor activity / positive regulation of G1/S transition of mitotic cell cycle / response to amino acid / 'de novo' pyrimidine nucleobase biosynthetic process / positive regulation of epithelial to mesenchymal transition / heart morphogenesis / vascular endothelial cell response to laminar fluid shear stress / neuronal action potential / positive regulation of lipid biosynthetic process / cellular response to nutrient levels / regulation of cellular response to heat / positive regulation of lamellipodium assembly / cardiac muscle contraction / phagocytic vesicle / T cell costimulation / positive regulation of stress fiber assembly / positive regulation of endothelial cell proliferation / 14-3-3 protein binding / cytoskeleton organization / endomembrane system / negative regulation of autophagy / negative regulation of insulin receptor signaling pathway / cellular response to amino acid starvation / cellular response to starvation / positive regulation of glycolytic process / protein serine/threonine kinase activator activity / positive regulation of translation / regulation of signal transduction by p53 class mediator / Regulation of PTEN gene transcription / VEGFR2 mediated vascular permeability / post-embryonic development / response to nutrient levels / TP53 Regulates Metabolic Genes / regulation of actin cytoskeleton organization / phosphoprotein binding
Similarity search - Function
Raptor, N-terminal CASPase-like domain / Raptor N-terminal CASPase like domain / Raptor N-terminal CASPase like domain / Regulatory associated protein of TOR / 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 ...Raptor, N-terminal CASPase-like domain / Raptor N-terminal CASPase like domain / Raptor N-terminal CASPase like domain / Regulatory associated protein of TOR / 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 / HEAT repeat / HEAT repeat / : / 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 / 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-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase mTOR / Regulatory-associated protein of mTOR / Target of rapamycin complex subunit LST8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsAylett CHS / Sauer E / Imseng S / Boehringer D / Hall MN / Ban N / Maier T
CitationJournal: Science / Year: 2016
Title: Architecture of human mTOR complex 1.
Authors: Christopher H S Aylett / Evelyn Sauer / Stefan Imseng / Daniel Boehringer / Michael N Hall / Nenad Ban / Timm Maier /
Abstract: Target of rapamycin (TOR), a conserved protein kinase and central controller of cell growth, functions in two structurally and functionally distinct complexes: TORC1 and TORC2. Dysregulation of ...Target of rapamycin (TOR), a conserved protein kinase and central controller of cell growth, functions in two structurally and functionally distinct complexes: TORC1 and TORC2. Dysregulation of mammalian TOR (mTOR) signaling is implicated in pathologies that include diabetes, cancer, and neurodegeneration. We resolved the architecture of human mTORC1 (mTOR with subunits Raptor and mLST8) bound to FK506 binding protein (FKBP)-rapamycin, by combining cryo-electron microscopy at 5.9 angstrom resolution with crystallographic studies of Chaetomium thermophilum Raptor at 4.3 angstrom resolution. The structure explains how FKBP-rapamycin and architectural elements of mTORC1 limit access to the recessed active site. Consistent with a role in substrate recognition and delivery, the conserved amino-terminal domain of Raptor is juxtaposed to the kinase active site.
History
DepositionOct 23, 2015-
Header (metadata) releaseNov 11, 2015-
Map releaseDec 30, 2015-
UpdateJan 13, 2016-
Current statusJan 13, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5flc
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3213_mTO...

Downloads & links

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Map

FileDownload / File: emd_3213.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman mTOR complex 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 256 pix.
= 355.84 Å		1.39 Å/pix.
x 256 pix.
= 355.84 Å		1.39 Å/pix.
x 256 pix.
= 355.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.066 / Movie #1: 0.045
Minimum - Maximum-0.04557803 - 0.20396529
Average (Standard dev.)0.00100273 (±0.01044368)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 355.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z355.840355.840355.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0460.2040.001

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Supplemental data

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Sample components

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Entire : Human mTOR complex 1

EntireName: Human mTOR complex 1
Components
  • Sample: Human mTOR complex 1
  • Protein or peptide: mTOR
  • Protein or peptide: Raptor
  • Protein or peptide: mLST8

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Supramolecule #1000: Human mTOR complex 1

SupramoleculeName: Human mTOR complex 1 / type: sample / ID: 1000 / Oligomeric state: tetrameric / Number unique components: 3
Molecular weightTheoretical: 1 MDa

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Macromolecule #1: mTOR

MacromoleculeName: mTOR / type: protein_or_peptide / ID: 1 / Oligomeric state: Dimeric / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 290 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: 21 / Recombinant plasmid: Multibac
SequenceUniProtKB: Serine/threonine-protein kinase mTOR

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Macromolecule #2: Raptor

MacromoleculeName: Raptor / type: protein_or_peptide / ID: 2 / Oligomeric state: Dimeric / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 150 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: 21 / Recombinant plasmid: Multibac
SequenceUniProtKB: Regulatory-associated protein of mTOR

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Macromolecule #3: mLST8

MacromoleculeName: mLST8 / type: protein_or_peptide / ID: 3 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 40 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: 21 / Recombinant plasmid: Multibac
SequenceUniProtKB: Target of rapamycin complex subunit LST8

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8 / Details: 100 mM NaCl, 10 mM NaBicine, 1 mM TCEP
GridDetails: Quantifoil R2/2 with an additional thin carbon layer
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK I / Method: 4 second blotting

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 150,000 times magnification
DateMay 5, 2015
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 6299 / Average electron dose: 25 e/Å2
Details: Single movie frame readout. 7 frames per exposure. Drift corrected in post-processing. 4 images per hole.
Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 100719 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.9 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsPoor quality micrographs were rejected by eye, based on the extent and regularity of the Thon rings observed in the contrast transfer function. Estimation of the contrast transfer function was carried out for each image using CTFFIND3, particles were selected semi-automatically using boxer and batchboxer.
CTF correctionDetails: Each image
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: OTHER / Software - Name: CTFFIND3, RELION, 1.3
Details: For full details see the supplemental materials and methods in the accompanying publication which provides processing details and the classification schema.
Number images used: 309792

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Atomic model buiding 1

Initial modelPDB ID:

4jsn


Chain - #0 - Chain ID: B / Chain - #1 - Chain ID: D
SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: CC
Output model

PDB-5flc:
Architecture of human mTOR Complex 1 - 5.9 Angstrom reconstruction

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