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- PDB-9f43: cryo-EM structure of human LST2 bound to human mTOR complex 1, fo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9f43 | |||||||||
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Title | cryo-EM structure of human LST2 bound to human mTOR complex 1, focused on RAPTOR | |||||||||
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![]() | SIGNALING PROTEIN / MTOR / MTORC1 / LST2 / ZFYVE28 / EGFR / TOS | |||||||||
Function / homology | ![]() negative regulation of epidermal growth factor-activated receptor activity / positive regulation of pentose-phosphate shunt / TORC1 complex / TORC1 signaling / positive regulation of odontoblast differentiation / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / phosphatidylinositol-3-phosphate binding ...negative regulation of epidermal growth factor-activated receptor activity / positive regulation of pentose-phosphate shunt / TORC1 complex / TORC1 signaling / positive regulation of odontoblast differentiation / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / phosphatidylinositol-3-phosphate binding / protein serine/threonine kinase inhibitor activity / positive regulation of osteoclast differentiation / cellular response to osmotic stress / enzyme-substrate adaptor activity / positive regulation of transcription by RNA polymerase III / regulation of cell size / Macroautophagy / negative regulation of epidermal growth factor receptor signaling pathway / protein kinase activator activity / mTORC1-mediated signalling / social behavior / HSF1-dependent transactivation / positive regulation of TOR signaling / TOR signaling / cellular response to nutrient levels / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of lipid biosynthetic process / 14-3-3 protein binding / positive regulation of endothelial cell proliferation / cellular response to starvation / positive regulation of glycolytic process / negative regulation of autophagy / positive regulation of peptidyl-threonine phosphorylation / regulation of autophagy / Regulation of PTEN gene transcription / regulation of cell growth / TP53 Regulates Metabolic Genes / cellular response to glucose stimulus / cellular response to amino acid stimulus / small GTPase binding / cytoplasmic stress granule / positive regulation of peptidyl-serine phosphorylation / protein-macromolecule adaptor activity / early endosome membrane / cellular response to hypoxia / positive regulation of cell growth / lysosome / response to xenobiotic stimulus / lysosomal membrane / neuronal cell body / dendrite / DNA damage response / protein-containing complex binding / protein kinase binding / nucleoplasm / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.49 Å | |||||||||
![]() | Craigie, L.M. / Maier, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: mTORC1 phosphorylates and stabilizes LST2 to negatively regulate EGFR Authors: Battaglioni, S. / Craigie, L.M. / Filippini, S. / Maier, T. / Hall, M.N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 248.9 KB | Display | ![]() |
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PDB format | ![]() | 179.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 50182 ![]() 50181 ![]() 50183 ![]() 50184 ![]() 50253 ![]() 50254 ![]() 50255 ![]() 9f42C ![]() 9f44C ![]() 9f45C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 152764.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 96604.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: mTORC1 in complex with LST2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 281 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 43 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4719 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1057805 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 545524 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 7PEB Accession code: 7PEB / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refine LS restraints |
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