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- EMDB-1480: 3D structure of the canine 80S ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-1480
Title3D structure of the canine 80S ribosome
Map data3D volume of the canine 80S ribosome determined at 8.7 A resolution (Fsc 0.5), within the context of a ribosome-channel complex from ER membranes.
Sample
  • Sample: canine 80S ribosome
  • Complex: 80S ribosome
Keywordseukaryotic ribosome / protein translation / tRNA translocation / expansion segments
Biological speciesCanis lupus familiaris (dog)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsChandramouli P / Topf M / Menetret JF / Eswar N / Cannone JJ / Gutell R / Sali A / Akey CW
CitationJournal: Structure / Year: 2008
Title: Structure of the mammalian 80S ribosome at 8.7 A resolution.
Authors: Preethi Chandramouli / Maya Topf / Jean-François Ménétret / Narayanan Eswar / Jamie J Cannone / Robin R Gutell / Andrej Sali / Christopher W Akey /
Abstract: In this paper, we present a structure of the mammalian ribosome determined at approximately 8.7 A resolution by electron cryomicroscopy and single-particle methods. A model of the ribosome was ...In this paper, we present a structure of the mammalian ribosome determined at approximately 8.7 A resolution by electron cryomicroscopy and single-particle methods. A model of the ribosome was created by docking homology models of subunit rRNAs and conserved proteins into the density map. We then modeled expansion segments in the subunit rRNAs and found unclaimed density for approximately 20 proteins. In general, many conserved proteins and novel proteins interact with expansion segments to form an integrated framework that may stabilize the mature ribosome. Our structure provides a snapshot of the mammalian ribosome at the beginning of translation and lends support to current models in which large movements of the small subunit and L1 stalk occur during tRNA translocation. Finally, details are presented for intersubunit bridges that are specific to the eukaryotic ribosome. We suggest that these bridges may help reset the conformation of the ribosome to prepare for the next cycle of chain elongation.
History
DepositionFeb 24, 2008-
Header (metadata) releaseFeb 25, 2008-
Map releaseMar 31, 2009-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4v5z
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1480.jpg

Downloads & links

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Map

FileDownload / File: emd_1480.map.gz / Format: CCP4 / Size: 17.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D volume of the canine 80S ribosome determined at 8.7 A resolution (Fsc 0.5), within the context of a ribosome-channel complex from ER membranes.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.73 Å/pix.
x 168 pix.
= 458.64 Å		2.73 Å/pix.
x 168 pix.
= 458.64 Å		2.73 Å/pix.
x 168 pix.
= 458.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.73 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1.0 / Movie #1: 3.5
Minimum - Maximum-16.530899999999999 - 23.4467
Average (Standard dev.)0.177751 (±1.37771)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 458.64 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.732.732.73
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z458.640458.640458.640
α/β/γ90.00090.00090.000
start NX/NY/NZ-55-55-55
NX/NY/NZ111111111
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
D min/max/mean-16.53123.4470.178

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Supplemental data

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Sample components

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Entire : canine 80S ribosome

EntireName: canine 80S ribosome
Components
  • Sample: canine 80S ribosome
  • Complex: 80S ribosome

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Supramolecule #1000: canine 80S ribosome

SupramoleculeName: canine 80S ribosome / type: sample / ID: 1000
Details: Sample was monodisperse with some mild aggregation.
Oligomeric state: monomer / Number unique components: 1
Molecular weightTheoretical: 3.6 MDa

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Supramolecule #1: 80S ribosome

SupramoleculeName: 80S ribosome / type: complex / ID: 1 / Name.synonym: ribosome
Details: The ribosome structure was determined within a larger, ribosome-channel complex isolated from ER membranes.
Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Canis lupus familiaris (dog) / synonym: Dog
Molecular weightTheoretical: 3.6 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Details: 30mM Hepesm 50mM KAc, 10mM Mg acetate and 1.5% digitonin.
GridDetails: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: home made plunger. in cold room
Method: blot for 1 second

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Electron microscopy

MicroscopeFEI TECNAI 20
TemperatureAverage: 93 K
Detailsdata were collected on Oxford and a Gatan cryo-holders
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 4.5 µm / Number real images: 500 / Average electron dose: 20 e/Å2 / Details: Creoscitex Eversmart was used to scan negatives. / Od range: 1 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 51000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: eucentric / Specimen holder model: OTHER

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Image processing

DetailsParticles selected with Boxer
CTF correctionDetails: by micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN
Details: sep option equals 3 and setsf were used in the final cycle. a combined structure factor was used to correct for amplitudes in EMAN using the low resolution region from the images and the mid- ...Details: sep option equals 3 and setsf were used in the final cycle. a combined structure factor was used to correct for amplitudes in EMAN using the low resolution region from the images and the mid-resolution region from a low angle X-ray diffraction pattern.
Number images used: 78800
Final angle assignmentDetails: 2 degree steps between classes

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Atomic model buiding 1

Initial model(PDB ID:

1j5e

,

1s72

,

1giy
PDB Unreleased entry

,

1gix
PDB Unreleased entry

)
RefinementSpace: REAL
Output model

PDB-4v5z:
Structure of a mammalian 80S ribosome obtained by docking homology models of the RNA and proteins into an 8.7 A cryo-EM map

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