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Yorodumi- PDB-9f42: cryo-EM structure of LST2 TOS peptide bound to human mTOR complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9f42 | |||||||||
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Title | cryo-EM structure of LST2 TOS peptide bound to human mTOR complex 1, focused on RAPTOR | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / MTOR / MTORC1 / LST2 / ZFYVE28 / EGFR / TOS | |||||||||
Function / homology | Function and homology information negative regulation of epidermal growth factor-activated receptor activity / positive regulation of pentose-phosphate shunt / TORC1 complex / positive regulation of odontoblast differentiation / TORC1 signaling / negative regulation of epidermal growth factor receptor signaling pathway / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK ...negative regulation of epidermal growth factor-activated receptor activity / positive regulation of pentose-phosphate shunt / TORC1 complex / positive regulation of odontoblast differentiation / TORC1 signaling / negative regulation of epidermal growth factor receptor signaling pathway / 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 / positive regulation of G1/S transition of mitotic cell cycle / Macroautophagy / protein kinase activator activity / mTORC1-mediated signalling / social behavior / HSF1-dependent transactivation / TOR signaling / positive regulation of TOR signaling / cellular response to nutrient levels / positive regulation of lipid biosynthetic process / 14-3-3 protein binding / Regulation of PTEN gene transcription / positive regulation of endothelial cell proliferation / cellular response to starvation / positive regulation of glycolytic process / negative regulation of autophagy / cellular response to amino acid stimulus / positive regulation of peptidyl-threonine phosphorylation / regulation of autophagy / regulation of cell growth / TP53 Regulates Metabolic Genes / cellular response to glucose stimulus / small GTPase binding / cytoplasmic stress granule / positive regulation of peptidyl-serine phosphorylation / early endosome membrane / cellular response to hypoxia / positive regulation of cell growth / protein-macromolecule adaptor activity / lysosome / response to xenobiotic stimulus / lysosomal membrane / neuronal cell body / DNA damage response / dendrite / protein-containing complex binding / protein kinase binding / nucleoplasm / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å | |||||||||
Authors | Craigie, L.M. / Maier, T. | |||||||||
Funding support | Switzerland, European Union, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9f42.cif.gz | 229.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9f42.ent.gz | 174.9 KB | Display | PDB format |
PDBx/mmJSON format | 9f42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9f42_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 9f42_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 9f42_validation.xml.gz | 52.5 KB | Display | |
Data in CIF | 9f42_validation.cif.gz | 75.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/9f42 ftp://data.pdbj.org/pub/pdb/validation_reports/f4/9f42 | HTTPS FTP |
-Related structure data
Related structure data | 50181MC 9f43C 9f44C 9f45C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: RPTOR, KIAA1303, RAPTOR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8N122 |
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#2: Protein/peptide | Mass: 1660.733 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9HCC9 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: mTORC1 in complex with synthesised LST2 TOS peptide / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 48.43 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4470 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2126474 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1414765 / 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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