+Open data
-Basic information
Entry | Database: PDB / ID: 8fw5 | |||||||||
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Title | Chimeric HsGATOR1-SpGtr-SpLam complex | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / mTOR complex 1 (mTORC1) / Rag GTPase / Gtr GTPase / LAMTOR / GATOR1 / nutrient sensing | |||||||||
Function / homology | Function and homology information GATOR1 complex / aorta morphogenesis / TORC1 signaling / Amino acids regulate mTORC1 / cardiac muscle tissue development / negative regulation of TOR signaling / vacuolar membrane / ventricular septum development / negative regulation of kinase activity / roof of mouth development ...GATOR1 complex / aorta morphogenesis / TORC1 signaling / Amino acids regulate mTORC1 / cardiac muscle tissue development / negative regulation of TOR signaling / vacuolar membrane / ventricular septum development / negative regulation of kinase activity / roof of mouth development / positive regulation of autophagy / negative regulation of TORC1 signaling / cellular response to amino acid starvation / GTPase activator activity / small GTPase binding / lysosome / intracellular signal transduction / lysosomal membrane / protein-containing complex binding / perinuclear region of cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å | |||||||||
Authors | Tettoni, S.D. / Egri, S.B. / Doxsey, D.D. / Ouch, C. / Chang, J. / Song, K. / Xu, C. / Shen, K. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Structure / Year: 2023 Title: Structure of the Schizosaccharomyces pombe Gtr-Lam complex reveals evolutionary divergence of mTORC1-dependent amino acid sensing. Authors: Steven D Tettoni / Shawn B Egri / Dylan D Doxsey / Kristen Veinotte / Christna Ouch / Jeng-Yih Chang / Kangkang Song / Chen Xu / Kuang Shen / Abstract: mTORC1 is a protein kinase complex that controls cellular growth in response to nutrient availability. Amino acid signals are transmitted toward mTORC1 via the Rag/Gtr GTPases and their upstream ...mTORC1 is a protein kinase complex that controls cellular growth in response to nutrient availability. Amino acid signals are transmitted toward mTORC1 via the Rag/Gtr GTPases and their upstream regulators. An important regulator is LAMTOR, which localizes Rag/Gtr on the lysosomal/vacuole membrane. In human cells, LAMTOR consists of five subunits, but in yeast, only three or four. Currently, it is not known how variation of the subunit stoichiometry may affect its structural organization and biochemical properties. Here, we report a 3.1 Å-resolution structural model of the Gtr-Lam complex in Schizosaccharomyces pombe. We found that SpGtr shares conserved architecture as HsRag, but the intersubunit communication that coordinates nucleotide loading on the two subunits differs. In contrast, SpLam contains distinctive structural features, but its GTP-specific GEF activity toward SpGtr is evolutionarily conserved. Our results revealed unique evolutionary paths of the protein components of the mTORC1 pathway. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fw5.cif.gz | 603.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fw5.ent.gz | 468.2 KB | Display | PDB format |
PDBx/mmJSON format | 8fw5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/8fw5 ftp://data.pdbj.org/pub/pdb/validation_reports/fw/8fw5 | HTTPS FTP |
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-Related structure data
Related structure data | 29497MC 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
-GATOR complex protein ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 181325.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DEPDC5, KIAA0645 / Production host: Homo sapiens (human) / References: UniProt: O75140 |
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#2: Protein | Mass: 45799.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NPRL2, TUSC4 / Production host: Homo sapiens (human) / References: UniProt: Q8WTW4 |
#3: Protein | Mass: 65769.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NPRL3, C16orf35, CGTHBA, MARE / Production host: Homo sapiens (human) / References: UniProt: Q12980 |
-GTP-binding protein ... , 2 types, 2 molecules DE
#4: Protein | Mass: 36500.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
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#5: Protein | Mass: 35547.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
-Schizosaccharomyces pombe ... , 4 types, 4 molecules FGHI
#6: Protein | Mass: 43686.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
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#7: Protein | Mass: 19830.908 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
#8: Protein | Mass: 12707.468 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
#9: Protein | Mass: 8984.198 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
-Non-polymers , 3 types, 4 molecules
#10: Chemical | #11: Chemical | ChemComp-AF3 / | #12: Chemical | ChemComp-MG / | |
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-Details
Has ligand of interest | Y |
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-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: Chimeric HsGATOR1-SpGtr-SpLam complex / Type: COMPLEX / Entity ID: #1-#9 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.42 MDa / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50.7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 659887 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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