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- EMDB-1395: Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo... -

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Basic information

Entry
Database: EMDB / ID: EMD-1395
TitleIncorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy.
Map dataCryo-EM map of E.coli 70S ribosome
Sample
  • Sample: 70S Post-initiation complex with fMettRNAfMet
  • Complex: Post-initiation Complex
  • RNA: tRNATransfer RNA
  • RNA: mRNAMessenger RNA
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.8 Å
AuthorsValle M / Zavialov A / Li W / Stagg SM / Sengupta J / Nielsen RC / Nissen P / Harvey SC / Ehrenberg M / Frank J
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
DepositionJul 27, 2007-
Header (metadata) releaseAug 2, 2007-
Map releaseAug 2, 2007-
UpdateOct 1, 2014-
Current statusOct 1, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 26
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 26
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1395.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of E.coli 70S ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.82 Å/pix.
x 130 pix.
= 366.6 Å
2.82 Å/pix.
x 130 pix.
= 366.6 Å
2.82 Å/pix.
x 130 pix.
= 366.6 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
Contour Level1: 58.799999999999997 / Movie #1: 26
Minimum - Maximum-102.870999999999995 - 238.061000000000007
Average (Standard dev.)3.24209 (±25.256499999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-65-65-65
Dimensions130130130
Spacing130130130
CellA=B=C: 366.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.822.822.82
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z366.600366.600366.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-65-65-65
NC/NR/NS130130130
D min/max/mean-102.871238.0613.242

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Supplemental data

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Sample components

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Entire : 70S Post-initiation complex with fMettRNAfMet

EntireName: 70S Post-initiation complex with fMettRNAfMet
Components
  • Sample: 70S Post-initiation complex with fMettRNAfMet
  • Complex: Post-initiation Complex
  • RNA: tRNATransfer RNA
  • RNA: mRNAMessenger RNA

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Supramolecule #1000: 70S Post-initiation complex with fMettRNAfMet

SupramoleculeName: 70S Post-initiation complex with fMettRNAfMet / type: sample / ID: 1000 / Number unique components: 3

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Supramolecule #1: Post-initiation Complex

SupramoleculeName: Post-initiation Complex / type: complex / ID: 1 / Ribosome-details: ribosome-prokaryote: ALL

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Macromolecule #1: tRNA

MacromoleculeName: tRNA / type: rna / ID: 1 / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #2: mRNA

MacromoleculeName: mRNA / type: rna / ID: 2 / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No
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 / Details: Rapid-freezing in liquid ethane

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49650 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: cryo transfer / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 93 K
Alignment procedureLegacy - Electron beam tilt params: 0
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: CTF correctionn of 3D map
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER package

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