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- EMDB-1310: Scaffolding as an organizing principle in trans-translation. The ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1310 | |||||||||
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Title | Scaffolding as an organizing principle in trans-translation. The roles of small protein B and ribosomal protein S1. | |||||||||
![]() | Cryo-EM map of Thermus thermophilus 70S ribosome bound with small protein B | |||||||||
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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![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 11.8 Å | |||||||||
![]() | Gillet R / Kaur S / Li W / Hallier M / Felden B / Frank J | |||||||||
![]() | ![]() Title: Scaffolding as an organizing principle in trans-translation. The roles of small protein B and ribosomal protein S1. Authors: Reynald Gillet / Sukhjit Kaur / Wen Li / Marc Hallier / Brice Felden / Joachim Frank / ![]() Abstract: A eubacterial ribosome stalled on a defective mRNA can be released through a quality control mechanism referred to as trans-translation, which depends on the coordinating binding actions of transfer- ...A eubacterial ribosome stalled on a defective mRNA can be released through a quality control mechanism referred to as trans-translation, which depends on the coordinating binding actions of transfer-messenger RNA, small protein B, and ribosome protein S1. By means of cryo-electron microscopy, we obtained a map of the complex composed of a stalled ribosome and small protein B, which appears near the decoding center. This result suggests that, when lacking a codon, the A-site on the small subunit is a target for small protein B. To investigate the role of S1 played in trans-translation, we obtained a cryo-electron microscopic map, including a stalled ribosome, transfer-messenger RNA, and small protein Bs but in the absence of S1. In this complex, several connections between the 30 S subunit and transfer-messenger RNA that appear in the +S1 complex are no longer found. We propose the unifying concept of scaffolding for the roles of small protein B and S1 in binding of transfer-messenger RNA to the ribosome during trans-translation, and we infer a pathway of sequential binding events in the initial phase of trans-translation. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.4 KB 11.4 KB | Display Display | ![]() |
Images | ![]() | 40.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ob7MC ![]() 1312C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cryo-EM map of Thermus thermophilus 70S ribosome bound with small protein B | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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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 / Details: the sample was monodisperse / Number unique components: 4 |
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Molecular weight | Theoretical: 2.3 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 / Recombinant expression: No |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 19 KDa |
-Macromolecule #2: tRNA
Macromolecule | Name: tRNA / type: rna / ID: 2 / Classification: TRANSFER / Structure: OTHER / Synthetic?: No |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #3: rRNA
Macromolecule | Name: rRNA / type: rna / ID: 3 / Classification: TRANSFER / Structure: OTHER / Synthetic?: No |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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 3, 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: 28 / 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: ![]() |
Electron optics | Calibrated magnification: 49696 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.12 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: cryo transfer / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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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: 11.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER package / Number images used: 37000 |