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Yorodumi- EMDB-1311: Cryo-EM visualization of transfer messenger RNA with two SmpBs in... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1311 | |||||||||
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Title | Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome. | |||||||||
Map data | Cryo-EM map of Thermus thermophilus 70S ribosome bound with tmRNA, two small protein B, and EF-Tu in the presence of S1 in solution. | |||||||||
Sample |
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Function / homology | trans-translation / SsrA-binding protein / SsrA-binding protein, conserved site / Small protein B / SmpB protein / SsrA-binding protein. / RNA binding / cytosol / SsrA-binding protein Function and homology information | |||||||||
Biological species | Thermus thermophilus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 13.6 Å | |||||||||
Authors | Kaur S / Gillet R / Li W / Gursky R / Frank J | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2006 Title: Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome. Authors: Sukhjit Kaur / Reynald Gillet / Wen Li / Richard Gursky / Joachim Frank / Abstract: In eubacterial translation, lack of a stop codon on the mRNA results in a defective, potentially toxic polypeptide stalled on the ribosome. Bacteria possess a specialized mRNA, called transfer ...In eubacterial translation, lack of a stop codon on the mRNA results in a defective, potentially toxic polypeptide stalled on the ribosome. Bacteria possess a specialized mRNA, called transfer messenger RNA (tmRNA), to rescue such a stalled system. tmRNA contains a transfer RNA (tRNA)-like domain (TLD), which enters the ribosome as a tRNA and places an ORF into the mRNA channel. This ORF codes for a signal marking the polypeptide for degradation and ends in a stop codon, leading to release of the faulty polypeptide and recycling of the ribosome. The binding of tmRNA to the stalled ribosome is mediated by small protein B (SmpB). By means of cryo-EM, we obtained a density map for the preaccommodated state of the tmRNA.SmpB.EF-Tu.70S ribosome complex with much improved definition for the tmRNA-SmpB complex, showing two SmpB molecules bound per ribosome, one toward the A site on the 30S subunit side and the other bound to the 50S subunit near the GTPase-associated center. tmRNA is strongly attached to the 30S subunit head by multiple contact sites, involving most of its pseudoknots and helices. The map clarifies that the TLD is located near helix 34 and protein S19 of the 30S subunit, rather than in the A site as tRNA for normal translation, so that the TLD is oriented toward the ORF. | |||||||||
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_1311.map.gz | 7.8 MB | EMDB map data format | |
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Header (meta data) | emd-1311-v30.xml emd-1311.xml | 11.4 KB 11.4 KB | Display Display | EMDB header |
Images | 1311.gif | 36.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1311 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1311 | HTTPS FTP |
-Validation report
Summary document | emd_1311_validation.pdf.gz | 236.9 KB | Display | EMDB validaton report |
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Full document | emd_1311_full_validation.pdf.gz | 236 KB | Display | |
Data in XML | emd_1311_validation.xml.gz | 6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1311 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1311 | HTTPS FTP |
-Related structure data
Related structure data | 2ob7M M: atomic model generated by this map |
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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_1311.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of Thermus thermophilus 70S ribosome bound with tmRNA, two small protein B, and EF-Tu in the presence of S1 in solution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.82 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: 2.4 MDa |
-Supramolecule #1: 70S Ribosome
Supramolecule | Name: 70S Ribosome / type: complex / ID: 1 / Ribosome-details: ribosome-prokaryote: ALL |
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Molecular weight | Experimental: 2.3 MDa |
-Macromolecule #1: small protein B
Macromolecule | Name: small protein B / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Recombinant expression: No |
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Source (natural) | Organism: Thermus thermophilus (bacteria) |
Molecular weight | Experimental: 19 KDa |
-Macromolecule #4: EF-Tu
Macromolecule | Name: EF-Tu / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: Thermus thermophilus (bacteria) |
-Macromolecule #2: tmRNA
Macromolecule | Name: tmRNA / type: rna / ID: 2 / Classification: OTHER / Structure: OTHER / Synthetic?: No |
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Source (natural) | Organism: Thermus thermophilus (bacteria) |
-Macromolecule #3: tRNA
Macromolecule | Name: tRNA / type: rna / ID: 3 / Classification: TRANSFER / Structure: OTHER / Synthetic?: No |
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Source (natural) | Organism: Thermus thermophilus (bacteria) / synonym: tRNA |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: see Methods |
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Staining | Type: NEGATIVE / Details: No staining (Cryo-EM) |
Grid | Details: Quanti-foil grids coated with a thin carbon layer |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 279 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot Method: Blot for 5 seconds before plunging Rapid plunge freezing in liquid ethane |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Min: 93 K / Max: 93 K / Average: 93 K |
Alignment procedure | Legacy - Electron beam tilt params: 0 |
Date | Aug 13, 2004 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 27 / Average electron dose: 15 e/Å2 / Bits/pixel: 8 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 49696 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.635 µm / Nominal defocus min: 1.475 µm / Nominal magnification: 5000 |
Sample stage | Specimen holder: cryo transfer / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: CTF correctionn of 3D map |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER package / Number images used: 52829 |
-Atomic model buiding 1
Software | Name: O |
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Details | Protocol: Rigid Body. manual fitting with O |
Refinement | Protocol: RIGID BODY FIT |
Output model | PDB-2ob7: |