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- EMDB-5198: 3D reconstruction of negatively stained human raptor -

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Basic information

Entry
Database: EMDB / ID: EMD-5198
Title3D reconstruction of negatively stained human raptor
Map dataDensity map of human raptor
Sample
  • Sample: Purified human raptor
  • Protein or peptide: raptor
Keywordsmetabolic role
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 28.0 Å
AuthorsYip CK / Murata K / Walz T / Sabatini DM / Kang SA
CitationJournal: Mol Cell / Year: 2010
Title: Structure of the human mTOR complex I and its implications for rapamycin inhibition.
Authors: Calvin K Yip / Kazuyoshi Murata / Thomas Walz / David M Sabatini / Seong A Kang /
Abstract: The mammalian target of rapamycin complex 1 (mTORC1) regulates cell growth in response to the nutrient and energy status of the cell, and its deregulation is common in human cancers. Little is known ...The mammalian target of rapamycin complex 1 (mTORC1) regulates cell growth in response to the nutrient and energy status of the cell, and its deregulation is common in human cancers. Little is known about the overall architecture and subunit organization of this essential signaling complex. We have determined the three-dimensional (3D) structure of the fully assembled human mTORC1 by cryo-electron microscopy (cryo-EM). Our analyses reveal that mTORC1 is an obligate dimer with an overall rhomboid shape and a central cavity. The dimeric interfaces are formed by interlocking interactions between the mTOR and raptor subunits. Extended incubation with FKBP12-rapamycin compromises the structural integrity of mTORC1 in a stepwise manner, leading us to propose a model in which rapamycin inhibits mTORC1-mediated phosphorylation of 4E-BP1 and S6K1 through different mechanisms.
History
DepositionApr 28, 2010-
Header (metadata) releaseMay 5, 2010-
Map releaseJun 10, 2010-
UpdateJan 10, 2011-
Current statusJan 10, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5198_1.tif

Downloads & links

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Map

FileDownload / File: emd_5198.map.gz / Format: CCP4 / Size: 825.2 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity map of human raptor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.48 Å/pix.
x 60 pix.
= 268.8 Å		4.48 Å/pix.
x 60 pix.
= 268.8 Å		4.48 Å/pix.
x 60 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.48 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.6 / Movie #1: 1.6
Minimum - Maximum-4.86464 - 6.46397
Average (Standard dev.)-0.393163 (±0.435864)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-30-30-30
Dimensions606060
Spacing606060
CellA=B=C: 268.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.484.484.48
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z268.800268.800268.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-30-30-30
NC/NR/NS606060
D min/max/mean-4.8656.464-0.393

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Supplemental data

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Sample components

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Entire : Purified human raptor

EntireName: Purified human raptor
Components
  • Sample: Purified human raptor
  • Protein or peptide: raptor

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Supramolecule #1000: Purified human raptor

SupramoleculeName: Purified human raptor / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: raptor

MacromoleculeName: raptor / type: protein_or_peptide / ID: 1 / Name.synonym: raptor / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human / Cell: HEK-293T / Location in cell: cytoplasm
Molecular weightTheoretical: 150 KDa
Recombinant expressionOrganism: Mammalian cells

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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

Concentration0.05 mg/mL
BufferpH: 7.5 / Details: 50mM HEPES, 150mM NaCl
StainingType: NEGATIVE
Details: protein solution was diluted 5x with buffer and adsorbed onto grids for 30 seconds before staining with 0.75% uranyl formate
GridDetails: 400 mesh copper
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
DateDec 1, 2007
Image recordingCategory: FILM / Film or detector model: GENERIC IMAGE PLATES / Digitization - Scanner: OTHER / Digitization - Sampling interval: 50 µm / Number real images: 83
Tilt angle min0
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 67000
Sample stageSpecimen holder: side entry room temperature holder / Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle max: 60

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Image processing

DetailsParticles were picked manually
CTF correctionDetails: each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, FREALIGN
Details: final map was resolution filtered to 28.0 Angstroms
Number images used: 1993
Final angle assignmentDetails: SPIDER:theta 45 degrees, phi 45 degrees
Final two d classificationNumber classes: 50

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