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- EMDB-5141: Ab initio reconstruction of the E. coli 70S ribosome complex (70S... -

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Basic information

Entry
Database: EMDB / ID: EMD-5141
TitleAb initio reconstruction of the E. coli 70S ribosome complex (70S-fMet-tRNAfMet-Phe-tRNAPhe-EF-Tu-GDP-kirromycin) via the asymmetric random-model method.
Map dataThis is a ab initio starting model for the E. coli 70S ribosome complex (70S-fMet-tRNAfMet-Phe-tRNAPhe-EF-Tu-GDP-kirromycin)
Sample
  • Sample: E. coli 70S ribosome complex, 70S-fMet-tRNAfMet-Phe-tRNAPhe-EF-Tu-GDP-kirromycin
  • Complex: 70S ribosome complex
KeywordsRandom-model method / ab initio reconstruction / E. coli 70S ribosome
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 23.0 Å
AuthorsSanz E / Stewart AB / Belnap DM
CitationJournal: Nat Struct Biol / Year: 2003
Title: Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy.
Authors: Mikel Valle / Andrey Zavialov / Wen Li / Scott M Stagg / Jayati Sengupta / Rikke C Nielsen / Poul Nissen / Stephen C Harvey / Måns Ehrenberg / Joachim Frank /
Abstract: Aminoacyl-tRNAs (aa-tRNAs) are delivered to the ribosome as part of the ternary complex of aa-tRNA, elongation factor Tu (EF-Tu) and GTP. Here, we present a cryo-electron microscopy (cryo-EM) study, ...Aminoacyl-tRNAs (aa-tRNAs) are delivered to the ribosome as part of the ternary complex of aa-tRNA, elongation factor Tu (EF-Tu) and GTP. Here, we present a cryo-electron microscopy (cryo-EM) study, at a resolution of approximately 9 A, showing that during the incorporation of the aa-tRNA into the 70S ribosome of Escherichia coli, the flexibility of aa-tRNA allows the initial codon recognition and its accommodation into the ribosomal A site. In addition, a conformational change observed in the GTPase-associated center (GAC) of the ribosomal 50S subunit may provide the mechanism by which the ribosome promotes a relative movement of the aa-tRNA with respect to EF-Tu. This relative rearrangement seems to facilitate codon recognition by the incoming aa-tRNA, and to provide the codon-anticodon recognition-dependent signal for the GTPase activity of EF-Tu. From these new findings we propose a mechanism that can explain the sequence of events during the decoding of mRNA on the ribosome.
History
DepositionNov 21, 2009-
Header (metadata) releaseApr 26, 2010-
Map releaseApr 26, 2010-
UpdateMar 6, 2013-
Current statusMar 6, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00141
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.00141
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5141_1.tif

Downloads & links

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Map

FileDownload / File: emd_5141.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a ab initio starting model for the E. coli 70S ribosome complex (70S-fMet-tRNAfMet-Phe-tRNAPhe-EF-Tu-GDP-kirromycin)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.82 Å/pix.
x 129 pix.
= 363.78 Å		2.82 Å/pix.
x 129 pix.
= 363.78 Å		2.82 Å/pix.
x 129 pix.
= 363.78 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00141 / Movie #1: 0.00141
Minimum - Maximum-0.00699515 - 0.00788587
Average (Standard dev.)0.00002563 (±0.00085812)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions129129129
Spacing129129129
CellA=B=C: 363.78 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.822.822.82
M x/y/z129129129
origin x/y/z0.0000.0000.000
length x/y/z363.780363.780363.780
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS129129129
D min/max/mean-0.0070.0080.000

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Supplemental data

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Sample components

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Entire : E. coli 70S ribosome complex, 70S-fMet-tRNAfMet-Phe-tRNAPhe-EF-Tu...

EntireName: E. coli 70S ribosome complex, 70S-fMet-tRNAfMet-Phe-tRNAPhe-EF-Tu-GDP-kirromycin
Components
  • Sample: E. coli 70S ribosome complex, 70S-fMet-tRNAfMet-Phe-tRNAPhe-EF-Tu-GDP-kirromycin
  • Complex: 70S ribosome complex

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Supramolecule #1000: E. coli 70S ribosome complex, 70S-fMet-tRNAfMet-Phe-tRNAPhe-EF-Tu...

SupramoleculeName: E. coli 70S ribosome complex, 70S-fMet-tRNAfMet-Phe-tRNAPhe-EF-Tu-GDP-kirromycin
type: sample / ID: 1000 / Oligomeric state: One ribosome binds two tRNA and one EF-Tu / Number unique components: 6

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Supramolecule #1: 70S ribosome complex

SupramoleculeName: 70S ribosome complex / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / 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

VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingCategory: FILM / Film or detector model: GENERIC FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Phase-flipped per micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PFT3DR, Bsoft
Details: Random-model method. Angular step-size was initially set to 20 deg. in the first iteration and gradually decreased by 0.19 deg. in each successive iteration, until a lower limit of 1 deg. was reached.
Number images used: 10000

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