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Yorodumi- EMDB-3212: Architecture of human mTOR Complex 1 - 6.1 Angstrom reconstruction -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3212 | |||||||||
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Title | Architecture of human mTOR Complex 1 - 6.1 Angstrom reconstruction | |||||||||
Map data | Human mTOR complex 1 | |||||||||
Sample |
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Keywords | Rapamycin / 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 / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / TORC2 complex / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding ...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 / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / TORC2 complex / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / regulation of membrane permeability / heart valve morphogenesis / negative regulation of lysosome organization / nucleus localization / RNA polymerase III type 3 promoter sequence-specific DNA binding / TORC1 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / calcineurin-NFAT signaling cascade / regulation of osteoclast differentiation / voluntary musculoskeletal movement / TORC1 signaling / positive regulation of odontoblast differentiation / positive regulation of keratinocyte migration / cellular response to L-leucine / Amino acids regulate mTORC1 / MTOR signalling / cellular response to nutrient / cellular response to methionine / Energy dependent regulation of mTOR by LKB1-AMPK / regulation of autophagosome assembly / energy reserve metabolic process / negative regulation of cell size / ruffle organization / positive regulation of osteoclast differentiation / cellular response to osmotic stress / protein serine/threonine kinase inhibitor activity / enzyme-substrate adaptor activity / anoikis / cardiac muscle cell development / negative regulation of protein localization to nucleus / positive regulation of transcription by RNA polymerase III / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / positive regulation of actin filament polymerization / regulation of cell size / negative regulation of macroautophagy / positive regulation of oligodendrocyte differentiation / lysosome organization / Macroautophagy / positive regulation of myotube differentiation / protein kinase activator activity / behavioral response to pain / oligodendrocyte differentiation / Constitutive Signaling by AKT1 E17K in Cancer / mTORC1-mediated signalling / germ cell development / CD28 dependent PI3K/Akt signaling / : / social behavior / HSF1-dependent transactivation / neuronal action potential / positive regulation of TOR signaling / response to amino acid / TOR signaling / 'de novo' pyrimidine nucleobase biosynthetic process / endomembrane system / regulation of macroautophagy / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of translational initiation / cellular response to nutrient levels / positive regulation of lamellipodium assembly / phagocytic vesicle / heart morphogenesis / positive regulation of lipid biosynthetic process / phosphorylation / positive regulation of epithelial to mesenchymal transition / cardiac muscle contraction / regulation of cellular response to heat / positive regulation of stress fiber assembly / cytoskeleton organization / 14-3-3 protein binding / positive regulation of endothelial cell proliferation / T cell costimulation / cellular response to starvation / cellular response to amino acid starvation / post-embryonic development / positive regulation of glycolytic process / protein serine/threonine kinase activator activity / negative regulation of autophagy / response to nutrient / response to nutrient levels / VEGFR2 mediated vascular permeability / regulation of signal transduction by p53 class mediator / positive regulation of peptidyl-threonine phosphorylation / Regulation of PTEN gene transcription / positive regulation of translation / regulation of autophagy / regulation of cell growth / regulation of actin cytoskeleton organization / cellular response to amino acid stimulus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.1 Å | |||||||||
Authors | Aylett CHS / Sauer E / Imseng S / Boehringer D / Hall MN / Ban N / Maier T | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3212.map.gz | 58.5 MB | EMDB map data format | |
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Header (meta data) | emd-3212-v30.xml emd-3212.xml | 12 KB 12 KB | Display Display | EMDB header |
Images | EMD-3212_mTORC1.png | 98.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3212 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3212 | HTTPS FTP |
-Validation report
Summary document | emd_3212_validation.pdf.gz | 218.8 KB | Display | EMDB validaton report |
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Full document | emd_3212_full_validation.pdf.gz | 218 KB | Display | |
Data in XML | emd_3212_validation.xml.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3212 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3212 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3212.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Human mTOR complex 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Human mTOR complex 1
Entire | Name: Human mTOR complex 1 |
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Components |
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-Supramolecule #1000: Human mTOR complex 1
Supramolecule | Name: Human mTOR complex 1 / type: sample / ID: 1000 / Oligomeric state: tetrameric / Number unique components: 3 |
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Molecular weight | Theoretical: 1 MDa |
-Macromolecule #1: mTOR
Macromolecule | Name: mTOR / type: protein_or_peptide / ID: 1 / Oligomeric state: Dimeric / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Theoretical: 290 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: 21 / Recombinant plasmid: Multibac |
Sequence | UniProtKB: Serine/threonine-protein kinase mTOR |
-Macromolecule #2: Raptor
Macromolecule | Name: Raptor / type: protein_or_peptide / ID: 2 / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Theoretical: 150 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: 21 / Recombinant plasmid: Multibac |
Sequence | UniProtKB: Regulatory-associated protein of mTOR |
-Macromolecule #3: mLST8
Macromolecule | Name: mLST8 / type: protein_or_peptide / ID: 3 / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Theoretical: 40 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: 21 / Recombinant plasmid: Multibac |
Sequence | UniProtKB: Target of rapamycin complex subunit LST8 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 / Details: 100 mM NaCl, 10 mM NaBicine, 1 mM TCEP |
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Grid | Details: Quantifoil R2/2 with an additional thin carbon layer |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK I / Method: 4 second blotting |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Average: 100 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 150,000 times magnification |
Date | May 5, 2015 |
Image recording | Category: 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | Poor 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. |
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CTF correction | Details: Each image |
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.1 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 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: B / Chain - #1 - Chain ID: D |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: CC |