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- EMDB-5234: transfer-messenger RNA in complex with the ribosome in the resume... -

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Basic information

Entry
Database: EMDB / ID: EMD-5234
Titletransfer-messenger RNA in complex with the ribosome in the resume state in E.coli cells
Map dataThis is the map of the tmRNA-ribosome complex in the resume state
Sample
  • Sample: transfer-messenger RNA bound to ribosome complex
  • Complex: ribosome
  • RNA: transfer-messenger RNA
Keywordstransfer-messenger RNA / trans-translation / small protein B
Function / homologytrans-translation / SsrA-binding protein / SsrA-binding protein, conserved site / Small protein B / SmpB protein / SsrA-binding protein. / rRNA binding / cytoplasm / SsrA-binding protein
Function and homology information
Biological speciesEscherichia coli (E. coli) / unidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.6 Å
AuthorsFu J / Hashem Y / Wower I / Lei J / Liao HY / Zwieb C / Wower J / Frank J
CitationJournal: EMBO J / Year: 2010
Title: Visualizing the transfer-messenger RNA as the ribosome resumes translation.
Authors: Jie Fu / Yaser Hashem / Iwona Wower / Jianlin Lei / Hstau Y Liao / Christian Zwieb / Jacek Wower / Joachim Frank /
Abstract: Bacterial ribosomes stalled by truncated mRNAs are rescued by transfer-messenger RNA (tmRNA), a dual-function molecule that contains a tRNA-like domain (TLD) and an internal open reading frame (ORF). ...Bacterial ribosomes stalled by truncated mRNAs are rescued by transfer-messenger RNA (tmRNA), a dual-function molecule that contains a tRNA-like domain (TLD) and an internal open reading frame (ORF). Occupying the empty A site with its TLD, the tmRNA enters the ribosome with the help of elongation factor Tu and a protein factor called small protein B (SmpB), and switches the translation to its own ORF. In this study, using cryo-electron microscopy, we obtained the first structure of an in vivo-formed complex containing ribosome and the tmRNA at the point where the TLD is accommodated into the ribosomal P site. We show that tmRNA maintains a stable 'arc and fork' structure on the ribosome when its TLD moves to the ribosomal P site and translation resumes on its ORF. Based on the density map, we built an atomic model, which suggests that SmpB interacts with the five nucleotides immediately upstream of the resume codon, thereby determining the correct selection of the reading frame on the ORF of tmRNA.
History
DepositionSep 20, 2010-
Header (metadata) releaseOct 4, 2010-
Map releaseOct 4, 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: 27
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 27
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3iz4
  • Surface level: 27
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3iz4
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5234_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5234.map.gz / Format: CCP4 / Size: 7.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the map of the tmRNA-ribosome complex in the resume state
Voxel sizeX=Y=Z: 3 Å
Density
Contour LevelBy AUTHOR: 27.0 / Movie #1: 27
Minimum - Maximum-102.9809494 - 247.154281620000006
Average (Standard dev.)5.55398035 (±25.628128050000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-62-62-62
Dimensions125125125
Spacing125125125
CellA=B=C: 375.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z333
M x/y/z125125125
origin x/y/z0.0000.0000.000
length x/y/z375.000375.000375.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S213
start NC/NR/NS-62-62-62
NC/NR/NS125125125
D min/max/mean-102.981247.1545.554

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Supplemental data

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Sample components

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Entire : transfer-messenger RNA bound to ribosome complex

EntireName: transfer-messenger RNA bound to ribosome complex
Components
  • Sample: transfer-messenger RNA bound to ribosome complex
  • Complex: ribosome
  • RNA: transfer-messenger RNA

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Supramolecule #1000: transfer-messenger RNA bound to ribosome complex

SupramoleculeName: transfer-messenger RNA bound to ribosome complex / type: sample / ID: 1000 / Number unique components: 2

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Supramolecule #1: ribosome

SupramoleculeName: ribosome / 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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Macromolecule #1: transfer-messenger RNA

MacromoleculeName: transfer-messenger RNA / type: rna / ID: 1 / Classification: TRANSFER / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: unidentified (others)

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: blot for 5 seconds before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 100000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.26 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 59000
Sample stageSpecimen holder: cartridge / Specimen holder model: OTHER
TemperatureAverage: 82 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 2000 / Average electron dose: 24 e/Å2 / Bits/pixel: 16
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Volumes
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 20873

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