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Yorodumi- EMDB-50254: Cryo-EM structure of human LST2 bound to human mTOR complex 1, fo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50254 | |||||||||
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Title | Cryo-EM structure of human LST2 bound to human mTOR complex 1, focused on one protomer | |||||||||
Map data | ||||||||||
Sample |
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Keywords | MTOR / MTORC1 / LST2 / ZFYVE28 / EGFR / TOS / SIGNALING PROTEIN | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.75 Å | |||||||||
Authors | Craigie LM / Maier T | |||||||||
Funding support | Switzerland, European Union, 2 items
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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 LM / Filippini S / Maier T / Hall MN | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_50254.map.gz | 257.5 MB | EMDB map data format | |
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Header (meta data) | emd-50254-v30.xml emd-50254.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_50254_fsc.xml | 16.9 KB | Display | FSC data file |
Images | emd_50254.png | 28.2 KB | ||
Masks | emd_50254_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-50254.cif.gz | 4.2 KB | ||
Others | emd_50254_half_map_1.map.gz emd_50254_half_map_2.map.gz | 474.6 MB 474.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50254 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50254 | HTTPS FTP |
-Validation report
Summary document | emd_50254_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_50254_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_50254_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | emd_50254_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50254 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50254 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_50254.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_50254_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_50254_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_50254_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : mTORC1 in complex with LST2
Entire | Name: mTORC1 in complex with LST2 |
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Components |
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-Supramolecule #1: mTORC1 in complex with LST2
Supramolecule | Name: mTORC1 in complex with LST2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4719 / Average electron dose: 43.0 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: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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