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- EMDB-1067: Domain movements of elongation factor eEF2 and the eukaryotic 80S... -

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Basic information

Entry
Database: EMDB / ID: 1067
TitleDomain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
SampleRibosomal 80S-eEF2-sordarin complex from S. cerevisiae
SourceSaccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
Map datamap
Methodsingle particle reconstruction, at 11.7 A resolution
AuthorsSpahn CM / Frank J
CitationEMBO J., 2004, 23, 1008-1019

EMBO J., 2004, 23, 1008-1019 StrPapers
Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
Christian M T Spahn / Maria G Gomez-Lorenzo / Robert A Grassucci / Rene Jørgensen / Gregers R Andersen / Roland Beckmann / Pawel A Penczek / Juan P G Ballesta / Joachim Frank

DateDeposition: Jan 5, 2004 / Header (metadata) release: Jan 6, 2004 / Map release: Jan 6, 2005 / Last update: Jan 5, 2004

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0003
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.0003
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_1067.map.gz (map file in CCP4 format, 7631 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
125 pix
2.93 A/pix
= 366.25 A
125 pix
2.93 A/pix
= 366.25 A
125 pix
2.93 A/pix
= 366.25 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.93 A
Density
Contour Level:0.000477, 0.0003 (movie #1):
Minimum - Maximum-0.00084646 - 0.00169185
Average (Standard dev.)1.69393e-05 (0.00020054)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions125125125
Origin-62-62-62
Limit626262
Spacing125125125
CellA=B=C: 366.25 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.932.932.93
M x/y/z125125125
origin x/y/z0.0000.0000.000
length x/y/z366.250366.250366.250
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ0052
NX/NY/NZ12812855
MAP C/R/S123
start NC/NR/NS-62-62-62
NC/NR/NS125125125
D min/max/mean-0.0010.0020.000

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Supplemental data

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Sample components

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Entire Ribosomal 80S-eEF2-sordarin complex from S. cerevisiae

EntireName: Ribosomal 80S-eEF2-sordarin complex from S. cerevisiae
Number of components: 2
MassTheoretical: 3.2 MDa

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Component #1: ribosome-eukaryote, 80S ribosome

Ribosome-eukaryoteName: 80S ribosome / Eukaryote: ALL / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /

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Component #2: protein, eEF2

ProteinName: eEF2 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /

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Experimental details

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Sample preparation

Specimen stateparticle
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 52000 X (calibrated) / Astigmatism: 100,000 X magnification / Cs: 2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderHolder: Oxford, cryo-transfer 3500 / Model: GATAN LIQUID NITROGEN / Temperature: 93 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 86 / Scanner: ZEISS SCAI / Bit depth: 12

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: back projection / Software: SPIDER / CTF correction: defocus group volumes / Resolution: 11.7 A / Resolution method: FSC 0.5

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Atomic model buiding

Output model

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