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- EMDB-5224: Human 80S ribosome in situ, untreated -

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Basic information

Entry
Database: EMDB / ID: 5224
TitleHuman 80S ribosome in situ, untreated
Keywordshuman 80S ribosome / puromycin / in situ / cytosol / polysome / polyribosome / protein synthesis / translation / 3D cryoEM / tomography / cellular tomography
SampleHuman 80S ribosome in situ, untreated
SourceHomo sapiens / human
Map dataThis is a map of a tomographic average of a human 80S ribosome in situ
Methodsubtomogram averaging, at 39 Å resolution
AuthorsBrandt F / Carlson L-A / Hartl FU / Baumeister W / Grunewald K
CitationMol. Cell, 2010, 39, 560-569

Mol. Cell, 2010, 39, 560-569 Yorodumi Papers
The three-dimensional organization of polyribosomes in intact human cells.
Florian Brandt / Lars-Anders Carlson / F Ulrich Hartl / Wolfgang Baumeister / Kay Grünewald

DateDeposition: Aug 10, 2010 / Header (metadata) release: Dec 9, 2010 / Map release: Dec 9, 2010 / Last update: Mar 6, 2013

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.9
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.9
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_5224.map.gz (map file in CCP4 format, 433 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
48 pix
8.21 Å/pix.
= 394.08 Å
48 pix
8.21 Å/pix.
= 394.08 Å
48 pix
8.21 Å/pix.
= 394.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 8.21 Å
Density
Contour Level:0.9 (by author), 0.9 (movie #1):
Minimum - Maximum-2.09170914 - 4.06884241
Average (Standard dev.)0E-8 (0.99999547)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions484848
Origin000
Limit474747
Spacing484848
CellA=B=C: 394.08002 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.218.218.21
M x/y/z484848
origin x/y/z0.0000.0000.000
length x/y/z394.080394.080394.080
α/β/γ90.00090.00090.000
start NX/NY/NZ-99-99-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS484848
D min/max/mean-2.0924.069-0.000

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Supplemental data

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Sample components

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Entire Human 80S ribosome in situ, untreated

EntireName: Human 80S ribosome in situ, untreated / Details: Cytosolic ribosomes in situ / Number of components: 1
Oligomeric State: One 80S ribosome within mixed cellular polysomes
MassMeasured by: Sedimentation, 80S

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Component #1: ribosome-eukaryote, cytosolic 80S ribosome

Ribosome-eukaryoteName: cytosolic 80S ribosome / Eukaryote: ALL / Recombinant expression: No
SourceSpecies: Homo sapiens / human

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: Cellular medium, DMEM (Gibco) supplemented with 10% foetal calf serum, 37C and 5% CO2
pH: 7.5
Support filmC-flat 2/1, holey carbon gold grid
StainingCells grown on grids, vitrification
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 77 K / Method: Blot for 2 s before plunging
Details: Vitrification instrument: plunger. Vitrification carried out in air

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM300FEG/T / Date: Jul 7, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 80 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 17500 X (nominal), 17500 X (calibrated)
Astigmatism: objective lens astigmatism was corrected at 50,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 5000 - 7000 nm / Energy filter: GIF2002 / Energy window: 0-20 eV
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder.
Model: GATAN LIQUID NITROGEN / Tilt Angle: -65 - 65 deg. / Temperature: 77 K ( 77 - K)
CameraDetector: GATAN MULTISCAN

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Image processing

ProcessingMethod: subtomogram averaging / Number of subtomograms: 1911 / Applied symmetry: C1 (asymmetric) / Number of class averages: 1
Details: Individual particle subvolumes were automatically selected by CCC threshold.
3D reconstructionAlgorithm: weighted back-projection / Software: EM / Details: exact weighting / Resolution: 39 Å / Resolution method: FSC 0.5

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