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Yorodumi- EMDB-7072: RagA/RagC:Ragulator complex structure determined by single partic... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7072 | |||||||||
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Title | RagA/RagC:Ragulator complex structure determined by single particle negative stain electron microscopy | |||||||||
Map data | RagA/RagC Ragulator complex determined by single particle negative stain electron microscopy | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 16.2 Å | |||||||||
Authors | Morris KL / Su M / Kim DJ / Fu Y / Lawrence R / Stjepanovic G / Zoncu R / Hurley JH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Mol Cell / Year: 2017 Title: Hybrid Structure of the RagA/C-Ragulator mTORC1 Activation Complex. Authors: Ming-Yuan Su / Kyle L Morris / Do Jin Kim / Yangxue Fu / Rosalie Lawrence / Goran Stjepanovic / Roberto Zoncu / James H Hurley / Abstract: The lysosomal membrane is the locus for sensing cellular nutrient levels, which are transduced to mTORC1 via the Rag GTPases and the Ragulator complex. The crystal structure of the five-subunit human ...The lysosomal membrane is the locus for sensing cellular nutrient levels, which are transduced to mTORC1 via the Rag GTPases and the Ragulator complex. The crystal structure of the five-subunit human Ragulator at 1.4 Å resolution was determined. Lamtor1 wraps around the other four subunits to stabilize the assembly. The Lamtor2:Lamtor3 dimer stacks upon Lamtor4:Lamtor5 to create a platform for Rag binding. Hydrogen-deuterium exchange was used to map the Rag binding site to the outer face of the Lamtor2:Lamtor3 dimer and to the N-terminal intrinsically disordered region of Lamtor1. EM was used to reconstruct the assembly of the full-length RagA:RagC dimer bound to Ragulator at 16 Å resolution, revealing that the G-domains of the Rags project away from the Ragulator core. The combined structural model shows how Ragulator functions as a platform for the presentation of active Rags for mTORC1 recruitment, and might suggest an unconventional mechanism for Rag GEF activity. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7072.map.gz | 13.2 MB | EMDB map data format | |
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Header (meta data) | emd-7072-v30.xml emd-7072.xml | 9.2 KB 9.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7072_fsc.xml | 7 KB | Display | FSC data file |
Images | emd_7072.png | 55 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7072 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7072 | HTTPS FTP |
-Validation report
Summary document | emd_7072_validation.pdf.gz | 78.3 KB | Display | EMDB validaton report |
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Full document | emd_7072_full_validation.pdf.gz | 77.5 KB | Display | |
Data in XML | emd_7072_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7072 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7072 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_7072.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | RagA/RagC Ragulator complex determined by single particle negative stain electron microscopy | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : RagA/RagC:Ragulator
Entire | Name: RagA/RagC:Ragulator |
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Components |
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-Supramolecule #1: RagA/RagC:Ragulator
Supramolecule | Name: RagA/RagC:Ragulator / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Insect cell expression vector pTIE1 (others) |
Molecular weight | Theoretical: 150 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Staining | Type: NEGATIVE / Material: Uranyl Formate |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |