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- EMDB-1068: Three-dimensional structures of translating ribosomes by Cryo-EM. -

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Basic information

Entry
Database: EMDB / ID: EMD-1068
TitleThree-dimensional structures of translating ribosomes by Cryo-EM.
Map data3D reconstruction of inactive 70S E. coli ribosome
Sample
  • Sample: 70S E. coli ribosome
  • Complex: E. coli 30S subunit
  • Complex: E. coli 50S subunit
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.4 Å
AuthorsGilbert RJC / Fucini P / Connell S / Fuller SD / Nierhaus KH / Robinson CV / Dobson CM / Stuart DI
CitationJournal: Mol Cell / Year: 2004
Title: Three-dimensional structures of translating ribosomes by Cryo-EM.
Authors: Robert J C Gilbert / Paola Fucini / Sean Connell / Stephen D Fuller / Knud H Nierhaus / Carol V Robinson / Christopher M Dobson / David I Stuart /
Abstract: Cryo-electron microscopy and image reconstruction techniques have been used to obtain three-dimensional maps for E. coli ribosomes stalled following translation of three representative proteins. ...Cryo-electron microscopy and image reconstruction techniques have been used to obtain three-dimensional maps for E. coli ribosomes stalled following translation of three representative proteins. Comparisons of these electron density maps, at resolutions of between 13 and 16 A, with that of a nontranslating ribosome pinpoint specific structural differences in stalled ribosomes and identify additional material, including tRNAs and mRNA. In addition, the tunnel through the large subunit, the anticipated exit route of newly synthesized proteins, is partially occluded in all the stalled ribosome structures. This observation suggests that significant segments of the nascent polypeptide chains examined here could be located within an expanded tunnel, perhaps in a rudimentary globular conformation. Such behavior could be an important aspect of the folding of at least some proteins in the cellular environment.
History
DepositionMar 2, 2004-
Header (metadata) releaseMar 6, 2004-
Map releaseApr 28, 2004-
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: 1.090048913
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 1.090048913
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1068.gif

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Map

FileDownload / File: emd_1068.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of inactive 70S E. coli ribosome
Voxel sizeX=Y=Z: 3.33 Å
Density
Contour Level1: 1.18 / Movie #1: 1.0900489
Minimum - Maximum-2.73293 - 4.38113
Average (Standard dev.)-0.000000000351418 (±0.471883)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 426.24 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.333.333.33
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z426.240426.240426.240
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ128128128
MAP C/R/S312
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-2.7334.381-0.000

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Supplemental data

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Sample components

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Entire : 70S E. coli ribosome

EntireName: 70S E. coli ribosome
Components
  • Sample: 70S E. coli ribosome
  • Complex: E. coli 30S subunit
  • Complex: E. coli 50S subunit

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Supramolecule #1000: 70S E. coli ribosome

SupramoleculeName: 70S E. coli ribosome / type: sample / ID: 1000 / Details: The sample was monodisperse. / Oligomeric state: 30S subunit and 50S subunit / Number unique components: 2
Molecular weightExperimental: 2 MDa

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Supramolecule #1: E. coli 30S subunit

SupramoleculeName: E. coli 30S subunit / type: complex / ID: 1 / Name.synonym: 30S / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #2: E. coli 50S subunit

SupramoleculeName: E. coli 50S subunit / type: complex / ID: 2 / Name.synonym: 50S / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli)

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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

Concentration5.0 mg/mL
BufferDetails: 20 mM HEPES, 150 mM ammonium acetate, 6 mM magnesium acetate, 2 mM spermidine, 0.05 mM spermine and 4 mM 2-mercaptoethanol. Concentration of ribosomes expressed to A260 units.
GridDetails: 300 mesh copper grid with holey carbon film
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Standard unmodified guillotine plunger

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2 mm / Nominal defocus max: 3.915 µm / Nominal defocus min: 1.475 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 100 K
DateMay 1, 2000
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 12 / Od range: 5 / Bits/pixel: 8

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Image processing

CTF correctionDetails: Each negative dataset
Final angle assignmentDetails: SPIDER euler
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, IMAGIC, GAP, CNS, XPLOR
Details: Final maps were calculated from 12 individual datasets, with scaling in reciprocal space to crystallographic ribosome structures and correction for map anisotropy by B-factor weighting of amplitudes in XPLOR.
Number images used: 8238

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Atomic model buiding 1

SoftwareName: GAP
DetailsProtocol: Rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: R-factor and correlation coefficient

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