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Yorodumi- EMDB-1829: SecM-stalled ribosomes adopt an altered geometry at the peptidylt... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1829 | |||||||||
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Title | SecM-stalled ribosomes adopt an altered geometry at the peptidyltransferase center | |||||||||
Map data | SecM stalled ribosome | |||||||||
Sample |
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Keywords | SecM-stalled RNC | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 5.6 Å | |||||||||
Authors | Bhushan S / Hoffman T / Seidelt B / Frauenfeld J / Mielke T / Berninghausen O / Wilson D / Beckmann R | |||||||||
Citation | Journal: PLoS Biol / Year: 2011 Title: SecM-stalled ribosomes adopt an altered geometry at the peptidyl transferase center. Authors: Shashi Bhushan / Thomas Hoffmann / Birgit Seidelt / Jens Frauenfeld / Thorsten Mielke / Otto Berninghausen / Daniel N Wilson / Roland Beckmann / Abstract: As nascent polypeptide chains are synthesized, they pass through a tunnel in the large ribosomal subunit. Interaction between specific nascent chains and the ribosomal tunnel is used to induce ...As nascent polypeptide chains are synthesized, they pass through a tunnel in the large ribosomal subunit. Interaction between specific nascent chains and the ribosomal tunnel is used to induce translational stalling for the regulation of gene expression. One well-characterized example is the Escherichia coli SecM (secretion monitor) gene product, which induces stalling to up-regulate translation initiation of the downstream secA gene, which is needed for protein export. Although many of the key components of SecM and the ribosomal tunnel have been identified, understanding of the mechanism by which the peptidyl transferase center of the ribosome is inactivated has been lacking. Here we present a cryo-electron microscopy reconstruction of a SecM-stalled ribosome nascent chain complex at 5.6 Å. While no cascade of rRNA conformational changes is evident, this structure reveals the direct interaction between critical residues of SecM and the ribosomal tunnel. Moreover, a shift in the position of the tRNA-nascent peptide linkage of the SecM-tRNA provides a rationale for peptidyl transferase center silencing, conditional on the simultaneous presence of a Pro-tRNA(Pro) in the ribosomal A-site. These results suggest a distinct allosteric mechanism of regulating translational elongation by the SecM stalling peptide. | |||||||||
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_1829.map.gz | 15.7 MB | EMDB map data format | |
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Header (meta data) | emd-1829-v30.xml emd-1829.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
Images | 1829.tif | 968.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1829 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1829 | HTTPS FTP |
-Validation report
Summary document | emd_1829_validation.pdf.gz | 273.1 KB | Display | EMDB validaton report |
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Full document | emd_1829_full_validation.pdf.gz | 272.2 KB | Display | |
Data in XML | emd_1829_validation.xml.gz | 6.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1829 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1829 | HTTPS FTP |
-Related 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_1829.map.gz / Format: CCP4 / Size: 94.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | SecM stalled ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.237 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 : SecM-stalled RNC
Entire | Name: SecM-stalled RNC |
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Components |
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-Supramolecule #1000: SecM-stalled RNC
Supramolecule | Name: SecM-stalled RNC / type: sample / ID: 1000 / Details: no / Number unique components: 1 |
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Molecular weight | Experimental: 2.3 MDa / Theoretical: 2.3 MDa |
-Supramolecule #1: 70S
Supramolecule | Name: 70S / type: complex / ID: 1 / Name.synonym: 70S / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Experimental: 2.3 MDa / Theoretical: 2.3 MDa |
-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 Details: 20 mM Hepes Ph 7.0, 50 mM Pot Acetate, 6 mM Mag Acetate, 5 mM DTT, 500 ug/ml Chloroamphenicol, 0.05 % Nikkol, 0.5 % pill/ml, 0.1 U/ml RNAsin, 125 mM sucrose |
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Staining | Type: NEGATIVE / Details: native |
Grid | Details: 2 nM carbon coated 200 mesh Cu grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: 10 seconds for blotting |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Specialist optics | Energy filter - Name: FEI |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Number real images: 400 / Average electron dose: 25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 38900 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | Processed using Spider |
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CTF correction | Details: CTFFIND on Micrographs |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Number images used: 544000 |
-Atomic model buiding 1
Initial model | PDB ID: 2wwq |
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Software | Name: Chimera |
Details | Fitted manually using Chimera and Coot |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 2
Initial model | PDB ID: 2wwl |
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Software | Name: Chimera |
Details | Fitted manually using Chimera and Coot |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |