[English] 日本語
Yorodumi
- EMDB-5198: 3D reconstruction of negatively stained human raptor -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 5198
Title3D reconstruction of negatively stained human raptor
Map dataDensity map of human raptor
SamplePurified human raptor:
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

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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

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

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

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

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions606060
Origin-30-30-30
Limit292929
Spacing606060
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
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

-
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.
CameraDetector: GENERIC IMAGE PLATES

-
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

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more