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Yorodumi- EMDB-5234: transfer-messenger RNA in complex with the ribosome in the resume... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5234 | |||||||||
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Title | transfer-messenger RNA in complex with the ribosome in the resume state in E.coli cells | |||||||||
Map data | This is the map of the tmRNA-ribosome complex in the resume state | |||||||||
Sample |
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Keywords | transfer-messenger RNA / trans-translation / small protein B | |||||||||
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 | Escherichia coli (E. coli) / unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.6 Å | |||||||||
Authors | Fu J / Hashem Y / Wower I / Lei J / Liao HY / Zwieb C / Wower J / Frank J | |||||||||
Citation | Journal: 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 |
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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_5234.map.gz | 1.2 MB | EMDB map data format | |
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Header (meta data) | emd-5234-v30.xml emd-5234.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
Images | emd_5234_1.jpg | 96.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5234 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5234 | HTTPS FTP |
-Validation report
Summary document | emd_5234_validation.pdf.gz | 333.7 KB | Display | EMDB validaton report |
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Full document | emd_5234_full_validation.pdf.gz | 333.3 KB | Display | |
Data in XML | emd_5234_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5234 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5234 | HTTPS FTP |
-Related structure data
Related structure data | 3iz4MC 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_5234.map.gz / Format: CCP4 / Size: 7.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is the map of the tmRNA-ribosome complex in the resume state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3 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 : transfer-messenger RNA bound to ribosome complex
Entire | Name: transfer-messenger RNA bound to ribosome complex |
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Components |
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-Supramolecule #1000: transfer-messenger RNA bound to ribosome complex
Supramolecule | Name: transfer-messenger RNA bound to ribosome complex / type: sample / ID: 1000 / Number unique components: 2 |
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-Supramolecule #1: ribosome
Supramolecule | Name: ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: transfer-messenger RNA
Macromolecule | Name: transfer-messenger RNA / type: rna / ID: 1 / Classification: TRANSFER / Structure: SINGLE STRANDED / Synthetic?: No |
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Source (natural) | Organism: unidentified (others) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: blot for 5 seconds before plunging |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Average: 82 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification |
Image recording | Category: 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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 100000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder: cartridge / Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Volumes |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 20873 |