+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5198 | |||||||||
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Title | 3D reconstruction of negatively stained human raptor | |||||||||
Map data | Density map of human raptor | |||||||||
Sample |
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Keywords | metabolic role | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 28.0 Å | |||||||||
Authors | Yip CK / Murata K / Walz T / Sabatini DM / Kang SA | |||||||||
Citation | Journal: Mol Cell / Year: 2010 Title: Structure of the human mTOR complex I and its implications for rapamycin inhibition. Authors: Calvin K Yip / Kazuyoshi Murata / Thomas Walz / David M Sabatini / Seong A Kang / Abstract: The mammalian target of rapamycin complex 1 (mTORC1) regulates cell growth in response to the nutrient and energy status of the cell, and its deregulation is common in human cancers. Little is known ...The mammalian target of rapamycin complex 1 (mTORC1) regulates cell growth in response to the nutrient and energy status of the cell, and its deregulation is common in human cancers. Little is known about the overall architecture and subunit organization of this essential signaling complex. We have determined the three-dimensional (3D) structure of the fully assembled human mTORC1 by cryo-electron microscopy (cryo-EM). Our analyses reveal that mTORC1 is an obligate dimer with an overall rhomboid shape and a central cavity. The dimeric interfaces are formed by interlocking interactions between the mTOR and raptor subunits. Extended incubation with FKBP12-rapamycin compromises the structural integrity of mTORC1 in a stepwise manner, leading us to propose a model in which rapamycin inhibits mTORC1-mediated phosphorylation of 4E-BP1 and S6K1 through different mechanisms. | |||||||||
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_5198.map.gz | 392.8 KB | EMDB map data format | |
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Header (meta data) | emd-5198-v30.xml emd-5198.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
Images | emd_5198_1.tif | 755.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5198 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5198 | HTTPS FTP |
-Validation report
Summary document | emd_5198_validation.pdf.gz | 78.7 KB | Display | EMDB validaton report |
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Full document | emd_5198_full_validation.pdf.gz | 77.9 KB | Display | |
Data in XML | emd_5198_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5198 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5198 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5198.map.gz / Format: CCP4 / Size: 825.2 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Density map of human raptor | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.48 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 : Purified human raptor
Entire | Name: Purified human raptor |
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Components |
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-Supramolecule #1000: Purified human raptor
Supramolecule | Name: Purified human raptor / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1 |
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Molecular weight | Theoretical: 150 KDa |
-Macromolecule #1: raptor
Macromolecule | Name: raptor / type: protein_or_peptide / ID: 1 / Name.synonym: raptor / Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: human / Cell: HEK-293T / Location in cell: cytoplasm |
Molecular weight | Theoretical: 150 KDa |
Recombinant expression | Organism: Mammalian cells |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.05 mg/mL |
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Buffer | pH: 7.5 / Details: 50mM HEPES, 150mM NaCl |
Staining | Type: NEGATIVE Details: protein solution was diluted 5x with buffer and adsorbed onto grids for 30 seconds before staining with 0.75% uranyl formate |
Grid | Details: 400 mesh copper |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Date | Dec 1, 2007 |
Image recording | Category: FILM / Film or detector model: GENERIC IMAGE PLATES / Digitization - Scanner: OTHER / Digitization - Sampling interval: 50 µm / Number real images: 83 |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 67000 |
Sample stage | Specimen holder: side entry room temperature holder / Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle max: 60 |