[English] 日本語
![](img/lk-miru.gif)
- EMDB-1722: Ribosome dynamics and tRNA movement as visualized by time-resolve... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-1722 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Ribosome dynamics and tRNA movement as visualized by time-resolved electon cryomicroscopy | |||||||||
![]() | Substate of E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post2) | |||||||||
![]() |
| |||||||||
![]() | Ribosome / translation / translocation / tRNA | |||||||||
Function / homology | ![]() stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis ...stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded 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 / four-way junction DNA binding / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 17.0 Å | |||||||||
![]() | Fischer N / Konevega AL / Wintermeyer W / Rodnina MV / Stark H | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 7.4 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 10.6 KB 10.6 KB | Display Display | ![]() |
Images | ![]() | 180.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4v76M ![]() 1716C ![]() 1717C ![]() 1718C ![]() 1719C ![]() 1720C ![]() 1721C ![]() 1723C ![]() 1724C ![]() 1725C ![]() 1726C ![]() 1727C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Substate of E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post2) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : Substate of E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in inter...
Entire | Name: Substate of E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post2) |
---|---|
Components |
|
-Supramolecule #1000: Substate of E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in inter...
Supramolecule | Name: Substate of E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post2) type: sample / ID: 1000 / Number unique components: 4 |
---|---|
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 |
---|---|
Source (natural) | Organism: ![]() ![]() |
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 |
---|---|
Source (natural) | Organism: ![]() ![]() |
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 |
---|---|
Source (natural) | Organism: ![]() ![]() |
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 |
---|---|
Source (natural) | Organism: synthetic construct (others) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | 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 |
---|---|
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 |
---|---|
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 |
Electron beam | Acceleration voltage: 160 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 162740 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / 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 |
-
Image processing
CTF correction | Details: Local |
---|---|
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: 5656 |