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- EMDB-7072: RagA/RagC:Ragulator complex structure determined by single partic... -

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Basic information

Entry
Database: EMDB / ID: EMD-7072
TitleRagA/RagC:Ragulator complex structure determined by single particle negative stain electron microscopy
Map dataRagA/RagC Ragulator complex determined by single particle negative stain electron microscopy
Sample
  • Complex: RagA/RagC:Ragulator
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 16.2 Å
AuthorsMorris KL / Su M / Kim DJ / Fu Y / Lawrence R / Stjepanovic G / Zoncu R / Hurley JH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111730 United States
CitationJournal: 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
DepositionOct 11, 2017-
Header (metadata) releaseNov 15, 2017-
Map releaseNov 15, 2017-
UpdateJan 29, 2020-
Current statusJan 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.73
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.73
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7072.png

Downloads & links

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Map

FileDownload / File: emd_7072.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRagA/RagC Ragulator complex determined by single particle negative stain electron microscopy
Voxel sizeX=Y=Z: 1.5 Å
Density
Contour LevelBy AUTHOR: 1.73 / Movie #1: 1.73
Minimum - Maximum-0.3337062 - 2.7926908
Average (Standard dev.)0.04365978 (±0.24719733)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 288.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.51.51.5
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z288.000288.000288.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.3342.7930.044

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Supplemental data

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Sample components

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Entire : RagA/RagC:Ragulator

EntireName: RagA/RagC:Ragulator
Components
  • Complex: RagA/RagC:Ragulator

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Supramolecule #1: RagA/RagC:Ragulator

SupramoleculeName: RagA/RagC:Ragulator / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
Molecular weightTheoretical: 150 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
StainingType: NEGATIVE / Material: Uranyl Formate

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER / Details: cryosparc ab-initio
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 16.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 24061
FSC plot (resolution estimation)

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