+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29497 | |||||||||
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Title | Chimeric HsGATOR1-SpGtr-SpLam complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | mTOR complex 1 (mTORC1) / Rag GTPase / Gtr GTPase / LAMTOR / GATOR1 / nutrient sensing / SIGNALING PROTEIN | |||||||||
Function / homology | Function and homology information GATOR1 complex / aorta morphogenesis / TORC1 signaling / Amino acids regulate mTORC1 / cardiac muscle tissue development / vacuolar membrane / ventricular septum development / negative regulation of kinase activity / roof of mouth development / positive regulation of autophagy ...GATOR1 complex / aorta morphogenesis / TORC1 signaling / Amino acids regulate mTORC1 / cardiac muscle tissue development / 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 | single particle reconstruction / cryo EM / Resolution: 3.08 Å | |||||||||
Authors | Tettoni SD / Egri SB / Doxsey DD / Ouch C / Chang J / Song K / Xu C / Shen K | |||||||||
Funding support | United States, 2 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29497.map.gz | 197.4 MB | EMDB map data format | |
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Header (meta data) | emd-29497-v30.xml emd-29497.xml | 26.2 KB 26.2 KB | Display Display | EMDB header |
Images | emd_29497.png | 141.5 KB | ||
Others | emd_29497_half_map_1.map.gz emd_29497_half_map_2.map.gz | 194.3 MB 194.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29497 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29497 | HTTPS FTP |
-Validation report
Summary document | emd_29497_validation.pdf.gz | 853.7 KB | Display | EMDB validaton report |
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Full document | emd_29497_full_validation.pdf.gz | 853.2 KB | Display | |
Data in XML | emd_29497_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | emd_29497_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29497 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29497 | HTTPS FTP |
-Related structure data
Related structure data | 8fw5MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29497.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_29497_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_29497_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Chimeric HsGATOR1-SpGtr-SpLam complex
+Supramolecule #1: Chimeric HsGATOR1-SpGtr-SpLam complex
+Macromolecule #1: GATOR complex protein DEPDC5
+Macromolecule #2: GATOR complex protein NPRL2
+Macromolecule #3: GATOR complex protein NPRL3
+Macromolecule #4: GTP-binding protein Gtr1
+Macromolecule #5: GTP-binding protein Gtr2
+Macromolecule #6: Schizosaccharomyces pombe LAM1, Human LAMTOR1 ortholog
+Macromolecule #7: Schizosaccharomyces pombe LAM2, Human LAMTOR2 ortholog
+Macromolecule #8: Schizosaccharomyces pombe LAM3, Human LAMTOR3 ortholog
+Macromolecule #9: Schizosaccharomyces pombe LAM4, Human LAMTOR5 ortholog
+Macromolecule #10: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #11: ALUMINUM FLUORIDE
+Macromolecule #12: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 659887 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |