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Yorodumi- EMDB-1720: Ribosome dynamics and tRNA movement as visualized by time-resolve... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1720 | |||||||||
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Title | Ribosome dynamics and tRNA movement as visualized by time-resolved electron cryomicroscopy | |||||||||
Map data | Substate of E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre5) | |||||||||
Sample |
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Keywords | Ribosome / translation / translocation / tRNA | |||||||||
Function / homology | Function and homology information stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity ...stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / four-way junction DNA binding / negative regulation of translational initiation / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / DNA endonuclease activity / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / regulation of cell growth / maintenance of translational fidelity / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / ribosome biogenesis / regulation of translation / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / molecular adaptor activity / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 17.0 Å | |||||||||
Authors | Fischer N / Konevega AL / Wintermeyer W / Rodnina MV / Stark H | |||||||||
Citation | Journal: Nature / Year: 2010 Title: Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy. Authors: Niels Fischer / Andrey L Konevega / Wolfgang Wintermeyer / Marina V Rodnina / Holger Stark / Abstract: The translocation step of protein synthesis entails large-scale rearrangements of the ribosome-transfer RNA (tRNA) complex. Here we have followed tRNA movement through the ribosome during ...The translocation step of protein synthesis entails large-scale rearrangements of the ribosome-transfer RNA (tRNA) complex. Here we have followed tRNA movement through the ribosome during translocation by time-resolved single-particle electron cryomicroscopy (cryo-EM). Unbiased computational sorting of cryo-EM images yielded 50 distinct three-dimensional reconstructions, showing the tRNAs in classical, hybrid and various novel intermediate states that provide trajectories and kinetic information about tRNA movement through the ribosome. The structures indicate how tRNA movement is coupled with global and local conformational changes of the ribosome, in particular of the head and body of the small ribosomal subunit, and show that dynamic interactions between tRNAs and ribosomal residues confine the path of the tRNAs through the ribosome. The temperature dependence of ribosome dynamics reveals a surprisingly flat energy landscape of conformational variations at physiological temperature. The ribosome functions as a Brownian machine that couples spontaneous conformational changes driven by thermal energy to directed movement. | |||||||||
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_1720.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-1720-v30.xml emd-1720.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | image1720.png | 172.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1720 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1720 | HTTPS FTP |
-Related structure data
Related structure data | 4v74M 1716C 1717C 1718C 1719C 1721C 1722C 1723C 1724C 1725C 1726C 1727C 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_1720.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Substate of E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre5) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 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 : Substate of E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in hybri...
Entire | Name: Substate of E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre5) |
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Components |
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-Supramolecule #1000: Substate of E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in hybri...
Supramolecule | Name: Substate of E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre5) type: sample / ID: 1000 / Number unique components: 4 |
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Molecular weight | Theoretical: 2.5 MDa |
-Supramolecule #1: Ribosome
Supramolecule | Name: Ribosome / type: complex / ID: 1 / Name.synonym: E. coli 70S / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 2.5 MDa |
-Macromolecule #1: fMetVal-tRNAVal
Macromolecule | Name: fMetVal-tRNAVal / type: rna / ID: 1 / Name.synonym: peptidyl tRNA / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 25 KDa |
-Macromolecule #2: tRNAfMet
Macromolecule | Name: tRNAfMet / type: rna / ID: 2 / Name.synonym: deacylated tRNA / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 25 KDa |
-Macromolecule #3: m022 mRNA
Macromolecule | Name: m022 mRNA / type: rna / ID: 3 / Name.synonym: mRNA / Details: coding sequence AUGGUU / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes |
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Source (natural) | Organism: synthetic construct (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 Details: 50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 77 K / Instrument: HOMEMADE PLUNGER Details: Vitrification instrument: Custom-built CEVS. Dew-point temperature (temperature on the grid) adjusted to 18 degrees C Timed resolved state: Samples were vitrified at different time points along the reaction coordinate (1, 2, 5 and 20 minutes after addition of deacylated tRNAfMet to 70S-fMetVal-tRNAVal complexes) Method: Manual blotting for about 2 seconds |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Electron beam | Acceleration voltage: 160 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 162740 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 161000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Temperature | Average: 77 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification |
Image recording | Category: CCD / Film or detector model: GENERIC TVIPS (4k x 4k) / Average electron dose: 20 e/Å2 |
-Image processing
CTF correction | Details: Local |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC, custom, Spider Details: Final maps were calculated from 13 datasets acquired at different time points, computationally sorted into distinct substates Number images used: 3052 |