+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5189 | |||||||||
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Title | tmRNA-SmpB: a journey to the center of the bacterial ribosome | |||||||||
Map data | tmRNA-SmpB complex translocated in the bacterial ribosome P site | |||||||||
Sample |
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Keywords | TMRNA / SMPB / RIBOSOME / TRANS-TRANSLATION | |||||||||
Function / homology | trans-translation / SsrA-binding protein / SsrA-binding protein, conserved site / Small protein B / SmpB protein / SsrA-binding protein. / rRNA binding / cytosol / SsrA-binding protein Function and homology information | |||||||||
Biological species | Thermus thermophilus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.0 Å | |||||||||
Authors | Weis F / Bron P / Giudice E / Rolland JP / Thomas D / Felden B / Gillet R | |||||||||
Citation | Journal: EMBO J / Year: 2010 Title: tmRNA-SmpB: a journey to the centre of the bacterial ribosome. Authors: Félix Weis / Patrick Bron / Emmanuel Giudice / Jean-Paul Rolland / Daniel Thomas / Brice Felden / Reynald Gillet / Abstract: Ribosomes mediate protein synthesis by decoding the information carried by messenger RNAs (mRNAs) and catalysing peptide bond formation between amino acids. When bacterial ribosomes stall on ...Ribosomes mediate protein synthesis by decoding the information carried by messenger RNAs (mRNAs) and catalysing peptide bond formation between amino acids. When bacterial ribosomes stall on incomplete messages, the trans-translation quality control mechanism is activated by the transfer-messenger RNA bound to small protein B (tmRNA-SmpB ribonucleoprotein complex). Trans-translation liberates the stalled ribosomes and triggers degradation of the incomplete proteins. Here, we present the cryo-electron microscopy structures of tmRNA-SmpB accommodated or translocated into stalled ribosomes. Two atomic models for each state are proposed. This study reveals how tmRNA-SmpB crosses the ribosome and how, as the problematic mRNA is ejected, the tmRNA resume codon is placed onto the ribosomal decoding site by new contacts between SmpB and the nucleotides upstream of the tag-encoding sequence. This provides a structural basis for the transit of the large tmRNA-SmpB complex through the ribosome and for the means by which the tmRNA internal frame is set for translation to resume. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5189.map.gz | 1.4 MB | EMDB map data format | |
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Header (meta data) | emd-5189-v30.xml emd-5189.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
Images | emd_5189_1.png | 273.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5189 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5189 | HTTPS FTP |
-Validation report
Summary document | emd_5189_validation.pdf.gz | 304.6 KB | Display | EMDB validaton report |
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Full document | emd_5189_full_validation.pdf.gz | 304.2 KB | Display | |
Data in XML | emd_5189_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5189 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5189 | HTTPS FTP |
-Related structure data
Related structure data | 3iyrMC 5188C 3iyqC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5189.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | tmRNA-SmpB complex translocated in the bacterial ribosome P site | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Thermus thermophilus 70S ribosome
Entire | Name: Thermus thermophilus 70S ribosome |
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Components |
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-Supramolecule #1000: Thermus thermophilus 70S ribosome
Supramolecule | Name: Thermus thermophilus 70S ribosome / type: sample / ID: 1000 / Number unique components: 5 |
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Molecular weight | Theoretical: 2.3 MDa |
-Supramolecule #1: 70S ribosome
Supramolecule | Name: 70S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: Thermus thermophilus (bacteria) |
Molecular weight | Theoretical: 2.3 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Details: 5mM Hepes-KOH (pH 7.5), 10mM NH4Cl, 10mM MgOAc, 50mM KCl, 0.1mM EDTA and 6mM BetaME |
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Grid | Details: Quantifoil holey-carbon grids previously glow-discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: OTHER / Details: Vitrification instrument: vitrobot / Method: Blot for 5 seconds before plunging |
-Electron microscopy
Microscope | JEOL 2200FS |
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Temperature | Average: 95 K |
Specialist optics | Energy filter - Name: JEOL / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | Jul 1, 2009 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 7.5 µm / Number real images: 163 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 45700 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC-V / Number images used: 70761 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B |
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Software | Name: UCSF-Chimera, mdff |
Details | Protocol: Rigid Body and flexible fitting. The domains were initially separately fitted by manual docking and then further optimized using mdff. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-Correlation |
Output model | PDB-3iyr: |
-Atomic model buiding 2
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B |
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Software | Name: UCSF-Chimera, mdff |
Details | Protocol: Rigid Body and flexible fitting. each subdomain (H2b-c, H5, pk1, pk2, pk3, pk4) were initially separately fitted by manual docking and then further optimized using mdff. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-Correlation |
Output model | PDB-3iyr: |