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- EMDB-5741: Single-particle Electron Microscopy Structure of the TRAPPIII Complex -

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Basic information

Entry
Database: EMDB / ID: 5741
TitleSingle-particle Electron Microscopy Structure of the TRAPPIII Complex
Map dataReconstruction of yeast TRAPPIII complex, filtered to 22 Angstrom resolution
SampleRecombinant TRAPPIII complex:
transport protein particle III
Keywordsautophagy
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / negative staining / 22 Å resolution
AuthorsTan D / Cai Y / Wang J / Zhang J / Menon S / Chou H-T / Ferro-Novick S / Reinisch KM / Walz T
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2013
Title: The EM structure of the TRAPPIII complex leads to the identification of a requirement for COPII vesicles on the macroautophagy pathway.
Authors: Dongyan Tan / Yiying Cai / Juan Wang / Jinzhong Zhang / Shekar Menon / Hui-Ting Chou / Susan Ferro-Novick / Karin M Reinisch / Thomas Walz
DateDeposition: Aug 12, 2013 / Header (metadata) release: Sep 4, 2013 / Map release: Nov 13, 2013 / Last update: Dec 11, 2013

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.507
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.507
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_5741.map.gz (map file in CCP4 format, 2001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
80 pix
4.48 Å/pix.
= 358.4 Å
80 pix
4.48 Å/pix.
= 358.4 Å
80 pix
4.48 Å/pix.
= 358.4 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:0.507 (by author), 0.507 (movie #1):
Minimum - Maximum-0.61211646 - 2.31793046
Average (Standard dev.)0.00571768 (0.11935551)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions808080
Origin000
Limit797979
Spacing808080
CellA=B=C: 358.4 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.484.484.48
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-0.6122.3180.006

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Supplemental data

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Sample components

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Entire Recombinant TRAPPIII complex

EntireName: Recombinant TRAPPIII complex / Number of components: 1 / Oligomeric State: oligomer
MassTheoretical: 254 kDa / Experimental: 254 kDa

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Component #1: protein, transport protein particle III

ProteinName: transport protein particle III / Oligomeric Details: monomer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 254 kDa / Experimental: 254 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pETDuet / Strain: BL21

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionSpecimen conc.: 0.4 mg/ml / Buffer solution: 20mM Tris-HCl, 300 mM NaCl, 1mM DTT / pH: 8
Support film200 mesh copper grids with thin carbon support, glow discharged
StainingGrids with adsorbed protein stained with 0.75% uranyl format for 20 seconds
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12 / Date: Dec 20, 2010 / Details: low dose setting
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 67000 X (nominal), 67000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 1500 nm
Specimen HolderModel: SIDE ENTRY, EUCENTRIC / Tilt Angle: 0 - 60 deg.
CameraDetector: GENERIC IMAGE PLATES

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Image acquisition

Image acquisitionNumber of digital images: 133 / Scanner: OTHER / Sampling size: 15 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 20 / Applied symmetry: C1 (asymmetric) / Number of projections: 1120
Details: Random Conical Tilt reconstruction using Spider scripts
3D reconstructionAlgorithm: random conical tilt / Software: Spider
Details: Final maps were calculated from a dataset of two class-averages
Resolution: 22 Å / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 2J3T

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