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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1849 | ||||||||||||
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Title | Cognate 70S-TC complex | ||||||||||||
![]() | Surface rendered view of Cognate 70S-TC complex | ||||||||||||
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![]() | ribosome / ternary complex / cognate | ||||||||||||
Function / homology | ![]() guanyl-nucleotide exchange factor complex / negative regulation of cytoplasmic translational initiation / translational elongation / guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding ...guanyl-nucleotide exchange factor complex / negative regulation of cytoplasmic translational initiation / translational elongation / guanosine tetraphosphate binding / 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 / translation elongation factor activity / translational termination / DnaA-L2 complex / four-way junction DNA binding / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / translational initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / DNA endonuclease activity / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / ribosomal large subunit assembly / 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 / tRNA binding / cytoplasmic translation / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / negative regulation of DNA-templated transcription / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.25 Å | ||||||||||||
![]() | Agirrezabala X / Schreiner E / Trabuco LG / Lei J / Ortiz-Meoz RF / Schulten K / Green R / Frank J | ||||||||||||
![]() | ![]() Title: Structural insights into cognate versus near-cognate discrimination during decoding. Authors: Xabier Agirrezabala / Eduard Schreiner / Leonardo G Trabuco / Jianlin Lei / Rodrigo F Ortiz-Meoz / Klaus Schulten / Rachel Green / Joachim Frank / ![]() Abstract: The structural basis of the tRNA selection process is investigated by cryo-electron microscopy of ribosomes programmed with UGA codons and incubated with ternary complex (TC) containing the near- ...The structural basis of the tRNA selection process is investigated by cryo-electron microscopy of ribosomes programmed with UGA codons and incubated with ternary complex (TC) containing the near-cognate Trp-tRNA(Trp) in the presence of kirromycin. Going through more than 350 000 images and employing image classification procedures, we find ∼8% in which the TC is bound to the ribosome. The reconstructed 3D map provides a means to characterize the arrangement of the near-cognate aa-tRNA with respect to elongation factor Tu (EF-Tu) and the ribosome, as well as the domain movements of the ribosome. One of the interesting findings is that near-cognate tRNA's acceptor stem region is flexible and CCA end becomes disordered. The data bring direct structural insights into the induced-fit mechanism of decoding by the ribosome, as the analysis of the interactions between small and large ribosomal subunit, aa-tRNA and EF-Tu and comparison with the cognate case (UGG codon) offers clues on how the conformational signals conveyed to the GTPase differ in the two cases. | ||||||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 54.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.8 KB 11.8 KB | Display Display | ![]() |
Images | ![]() | 1.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 351.2 KB | Display | ![]() |
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Full document | ![]() | 350.8 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4v6kMC ![]() 1850C ![]() 4v6lC 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 | Surface rendered view of Cognate 70S-TC complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.5 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 : Cognate 70S-TC complex
Entire | Name: Cognate 70S-TC complex |
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Components |
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-Supramolecule #1000: Cognate 70S-TC complex
Supramolecule | Name: Cognate 70S-TC complex / type: sample / ID: 1000 Details: 70S.fMet-tRNAfMet.EF-Tu.Trp-tRNATrp on cognate codon Oligomeric state: Monomeric / Number unique components: 4 |
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Molecular weight | Theoretical: 2.8 MDa / Method: Sedimentation |
-Supramolecule #1: 70S Ribosome
Supramolecule | Name: 70S Ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: fMet-tRNAfMet
Macromolecule | Name: fMet-tRNAfMet / type: rna / ID: 1 / Name.synonym: fMet-tRNAfMet / Classification: TRANSFER / Structure: SINGLE STRANDED / Synthetic?: No |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: CGCGGGGTGG AGCAGCCTGG TAGCTCGTCG GGCTCATAAC CCGAAGATCG TCGGTTCAAA TCCGGCCCCC GCAACCA |
-Macromolecule #3: Trp-tRNATrp
Macromolecule | Name: Trp-tRNATrp / type: rna / ID: 3 / Classification: TRANSFER / Structure: SINGLE STRANDED / Synthetic?: No |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: AGGGGCGTAG TTCAATTGGT AGAGCACCGG TCTCCAAAAC CGGGTGTTGG GAGTTCGAGT CTCTCCGCCC CTGCCA |
-Macromolecule #2: EF-Tu
Macromolecule | Name: EF-Tu / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.04 mg/mL |
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Buffer | pH: 7.5 Details: HiFi (50 mM Tris-HCl pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT) |
Vitrification | Cryogen name: NITROGEN / Chamber humidity: 90 % / Chamber temperature: 80 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 6 seconds |
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Electron microscopy
Microscope | FEI TECNAI F30 |
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Alignment procedure | Legacy - Astigmatism: Objective corrected at 100,000 times magnification |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 20 e/Å2 Details: Automated data collection system AutoEMation (CCD mag. 100000x) TVIPS TemCam-F415 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 58269 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: Defocus groups, Wiener filter |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.25 Å / Resolution method: OTHER / Software - Name: Spider / Number images used: 359223 |
-Atomic model buiding 1
Initial model | PDB ID: ![]() 2i2v |
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Software | Name: MDFF |
Details | Protocol: MD-based flexible fitting |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: RMSD, cross correlation |
Output model | ![]() PDB-4v6k: |