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- EMDB-1361: Structure of TOR and its complex with KOG1. -

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Basic information

Entry
Database: EMDB / ID: EMD-1361
TitleStructure of TOR and its complex with KOG1.
Map data3D reconstruction of the yeast TOR (target of rapamycin)protein complexed with KOG1
Sample
  • Sample: TOR-KOG1 complex
  • Protein or peptide: TOR
  • Protein or peptide: KOG1
Function / homologymolecular_function / Regulatory associated protein of TOR / HEAT repeat / 1-phosphatidylinositol-3-kinase activity
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 26.0 Å
AuthorsAdami A / Garcia-Alvarez B / Arias-Palomo E / Barford D / Llorca O
CitationJournal: Mol Cell / Year: 2007
Title: Structure of TOR and its complex with KOG1.
Authors: Alessandra Adami / Begoña García-Alvarez / Ernesto Arias-Palomo / David Barford / Oscar Llorca /
Abstract: The target of rapamycin (TOR) is a large (281 kDa) conserved Ser/Thr protein kinase that functions as a central controller of cell growth. TOR assembles into two distinct multiprotein complexes: ...The target of rapamycin (TOR) is a large (281 kDa) conserved Ser/Thr protein kinase that functions as a central controller of cell growth. TOR assembles into two distinct multiprotein complexes: TORC1 and TORC2. A defining feature of TORC1 is the interaction of TOR with KOG1 (Raptor in mammals) and its sensitivity to a rapamycin-FKBP12 complex. Here, we have reconstructed in three dimensions the 25 A resolution structures of endogenous budding yeast TOR1 and a TOR-KOG1 complex, using electron microscopy. TOR features distinctive N-terminal HEAT repeats that form a curved tubular-shaped domain that associates with the C-terminal WD40 repeat domain of KOG1. The N terminus of KOG1 is in proximity to the TOR kinase domain, likely functioning to bring substrates into the vicinity of the catalytic region. A model is proposed for the molecular architecture of the TOR-KOG1 complex explaining its sensitivity to rapamycin.
History
DepositionApr 26, 2007-
Header (metadata) releaseMay 24, 2007-
Map releaseJun 24, 2011-
UpdateSep 19, 2012-
Current statusSep 19, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1361.gif

Downloads & links

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Map

FileDownload / File: emd_1361.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of the yeast TOR (target of rapamycin)protein complexed with KOG1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.2 Å/pix.
x 72 pix.
= 302.4 Å		4.2 Å/pix.
x 72 pix.
= 302.4 Å		4.2 Å/pix.
x 72 pix.
= 302.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 5.3 / Movie #1: 5.1
Minimum - Maximum-5.26305199 - 11.93820858
Average (Standard dev.)-0.00000001 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions727272
Spacing727272
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.24.24.2
M x/y/z727272
origin x/y/z0.0000.0000.000
length x/y/z302.400302.400302.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS727272
D min/max/mean-5.26311.938-0.000

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Supplemental data

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Sample components

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Entire : TOR-KOG1 complex

EntireName: TOR-KOG1 complex
Components
  • Sample: TOR-KOG1 complex
  • Protein or peptide: TOR
  • Protein or peptide: KOG1

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Supramolecule #1000: TOR-KOG1 complex

SupramoleculeName: TOR-KOG1 complex / type: sample / ID: 1000
Oligomeric state: One monomer of TOR bound to one monomer of KOG1
Number unique components: 2
Molecular weightTheoretical: 457 KDa

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Macromolecule #1: TOR

MacromoleculeName: TOR / type: protein_or_peptide / ID: 1 / Name.synonym: target of rapamycin / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast / Cell: yeast
Molecular weightExperimental: 281 KDa
SequenceGO: 1-phosphatidylinositol-3-kinase activity / InterPro: HEAT repeat

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Macromolecule #2: KOG1

MacromoleculeName: KOG1 / type: protein_or_peptide / ID: 2 / Name.synonym: Kontroller of Growth 1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast
Molecular weightExperimental: 176 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant plasmid: pFA-6a-TAP-KanMX6
SequenceGO: molecular_function / InterPro: Regulatory associated protein of TOR

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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: 7.1
Details: 50mM HEPES-KOH pH7.1, 3mM DTT, 10% glycerol, 0.25% Tween 20 for TOR-KOG1, 150 mM KCl, 1 mM Mg acetate, 2 mM EGTA
StainingType: NEGATIVE / Details: 1% uranyl acetate
GridDetails: 400 mesh Copper/Palladium grid
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 1230
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.9 mm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER
Alignment procedureLegacy - Astigmatism: correction with FFT and CCD camera
DetailsMicroscope used - JEOL JEM-1230
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 10.5 µm
Details: images scanned with a MINOLTA Dimage Scan Multi Pro scanner at 2400 dpi and averaged to a final 4.2 angstroms per pixel at the specimen
Bits/pixel: 16

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Image processing

CTF correctionDetails: CTF for each micrograph was estimated using CTFIND3 and the phases flipped with BSOFT
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 5508

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Atomic model buiding 1

Initial modelPDB ID:

2g9a

SoftwareName: ADP_EM
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: R-factor

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