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- EMDB-3896: Cryo-EM Structure of Saccharomyces cerevisiae Target of Rapamycin... -

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Basic information

Entry
Database: EMDB / ID: 3896
TitleCryo-EM Structure of Saccharomyces cerevisiae Target of Rapamycin Complex 2
SampleTarget of rapamycin protein complex 2
SourceSaccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Map datarefined and postprocessed map
Methodsingle particle reconstruction, at 7.9 Å resolution
AuthorsKaruppasamy M / Kusmider B
CitationNat Commun, 2017, 8, 1729-1729

primary. Nat Commun, 2017, 8, 1729-1729 Yorodumi Papers
Cryo-EM structure of Saccharomyces cerevisiae target of rapamycin complex 2.
Manikandan Karuppasamy / Beata Kusmider / Taiana M Oliveira / Christl Gaubitz / Manoel Prouteau / Robbie Loewith / Christiane Schaffitzel

1. Mol. Cell, 2015, 58, 977-988 Yorodumi Papers
Molecular Basis of the Rapamycin Insensitivity of Target Of Rapamycin Complex 2.
Christl Gaubitz / Taiana M Oliveira / Manoel Prouteau / Alexander Leitner / Manikandan Karuppasamy / Georgia Konstantinidou / Delphine Rispal / Sandra Eltschinger / Graham C Robinson / Stéphane Thore / Ruedi Aebersold / Christiane Schaffitzel / Robbie Loewith

Validation ReportPDB-ID: 6emk

SummaryFull reportAbout validation report
DateDeposition: Oct 2, 2017 / Header (metadata) release: Oct 18, 2017 / Map release: Dec 6, 2017 / Last update: Dec 6, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0147
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.0147
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-6emk
  • Surface level: 0.0147
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6emk
  • Imaged by Jmol
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3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_3896.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.38 Å/pix.
= 441.6 Å
320 pix
1.38 Å/pix.
= 441.6 Å
320 pix
1.38 Å/pix.
= 441.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.38 Å
Density
Contour Level:0.0147 (by author), 0.0147 (movie #1):
Minimum - Maximum-0.043736793 - 0.10092282
Average (Standard dev.)0.0011989143 (0.0065768785)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 441.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z441.600441.600441.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0440.1010.001

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Supplemental data

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Sample components

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Entire Target of rapamycin protein complex 2

EntireName: Target of rapamycin protein complex 2 / Number of components: 6
MassTheoretical: 1.4 MDa

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Component #1: protein, Target of rapamycin protein complex 2

ProteinName: Target of rapamycin protein complex 2 / Recombinant expression: No
MassTheoretical: 1.4 MDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Source (engineered)Expression System: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #2: protein, Serine/threonine-protein kinase TOR2

ProteinName: Serine/threonine-protein kinase TOR2 / Recombinant expression: No
MassTheoretical: 281.915438 kDa
Source (engineered)Expression System: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #3: protein, Target of rapamycin complex subunit LST8

ProteinName: Target of rapamycin complex subunit LST8 / Recombinant expression: No
MassTheoretical: 34.077879 kDa
Source (engineered)Expression System: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #4: protein, Target of rapamycin complex 2 subunit TSC11

ProteinName: Target of rapamycin complex 2 subunit TSC11 / Recombinant expression: No
MassTheoretical: 25.804662 kDa
Source (engineered)Expression System: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #5: protein, Target of rapamycin complex 2 subunit AVO2

ProteinName: Target of rapamycin complex 2 subunit AVO2 / Recombinant expression: No
MassTheoretical: 47.206457 kDa
Source (engineered)Expression System: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #6: protein, Target of rapamycin complex 2 subunit AVO1

ProteinName: Target of rapamycin complex 2 subunit AVO1 / Recombinant expression: No
MassTheoretical: 131.565453 kDa
Source (engineered)Expression System: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 4 K / Humidity: 100 % / Details: 2 - 3 sec blotting

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 47 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 3500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 70 - 70 K)
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Image acquisition #1Number of digital images: 4189
Image acquisition #2Number of digital images: 2847

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 16190
3D reconstruction #1Software: RELION / Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF
3D reconstruction #2Software: RELION / Resolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 5FVM
Output model

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