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

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Basic information

Database: EMDB / ID: 5198
Title3D reconstruction of negatively stained human raptor
Map dataDensity map of human raptor
SamplePurified human raptor:
Keywordsmetabolic role
SourceHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / 28 Å resolution
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.
DateDeposition: Apr 28, 2010 / Header (metadata) release: May 5, 2010 / Map release: Jun 10, 2010 / Last update: Jan 10, 2011

Structure visualization

  • 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
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_5198.map.gz (map file in CCP4 format, 845 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
60 pix
4.48 Å/pix.
= 268.8 Å
60 pix
4.48 Å/pix.
= 268.8 Å
60 pix
4.48 Å/pix.
= 268.8 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.48 Å
Contour Level:1.6 (by author), 1.6 (movie #1):
Minimum - Maximum-4.86464 - 6.46397
Average (Standard dev.)-0.393163 (0.435864)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 268.8 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ-34-26-72
MAP C/R/S123
start NC/NR/NS-30-30-30
D min/max/mean-4.8656.464-0.393

Supplemental data

Sample components

Entire Purified human raptor

EntireName: Purified human raptor / Number of components: 1 / Oligomeric State: monomer
MassTheoretical: 150 kDa

Component #1: protein, raptor

ProteinName: raptor / a.k.a: raptor / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 150 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Mammalian cells
Source (natural)Location in cell: cytoplasm / Cell: HEK-293T

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionSpecimen conc.: 0.05 mg/ml / Buffer solution: 50mM HEPES, 150mM NaCl / pH: 7.5
Support film400 mesh copper
Stainingprotein solution was diluted 5x with buffer and adsorbed onto grids for 30 seconds before staining with 0.75% uranyl formate
VitrificationInstrument: NONE / Cryogen name: NONE

Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12 / Date: Dec 1, 2007
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
LensMagnification: 67000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 1500 nm
Specimen HolderHolder: side entry room temperature holder / Model: SIDE ENTRY, EUCENTRIC / Tilt Angle: 0 - 60 deg.

Image acquisition

Image acquisitionNumber of digital images: 83 / Scanner: OTHER / Sampling size: 50 microns

Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 50 / Number of projections: 1993 / Details: Particles were picked manually / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: random conical tilt / Euler angles: SPIDER:theta 45 degrees, phi 45 degrees / Software: SPIDER, FREALIGN / CTF correction: each particle
Details: final map was resolution filtered to 28.0 Angstroms
Resolution: 28 Å / Resolution method: FSC 0.5

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