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- EMDB-1565: Recognition of Phe-tRNAPhe, Trp-tRNATrp and : a common molecular ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1565 | |||||||||
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Title | Recognition of Phe-tRNAPhe, Trp-tRNATrp and : a common molecular mechanism for aminoacyl-tRNA selection revealed by cryo-EM | |||||||||
![]() | Trp-tRNA-EFTu-kir-GDP-70S ribosome | |||||||||
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![]() | protein translation / decoding / elongation factor Tu / ribosome | |||||||||
Function / homology | ![]() guanyl-nucleotide exchange factor complex / translational elongation / guanosine tetraphosphate binding / stringent response / misfolded RNA binding / Group I intron splicing / RNA folding / translation elongation factor activity / translational termination / positive regulation of RNA splicing ...guanyl-nucleotide exchange factor complex / translational elongation / guanosine tetraphosphate binding / stringent response / misfolded RNA binding / Group I intron splicing / RNA folding / translation elongation factor activity / translational termination / positive regulation of RNA splicing / maintenance of translational fidelity / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / GTP binding / RNA binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 9.0 Å | |||||||||
![]() | Li W / Agirrezabala X / Lei J / Bouakaz L / Brunelle JL / Ortiz-Meoz RF / Green R / Sanyal S / Ehrenberg M / Frank J | |||||||||
![]() | ![]() Title: Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM. Authors: Wen Li / Xabier Agirrezabala / Jianlin Lei / Lamine Bouakaz / Julie L Brunelle / Rodrigo F Ortiz-Meoz / Rachel Green / Suparna Sanyal / Måns Ehrenberg / Joachim Frank / ![]() Abstract: The accuracy of ribosomal translation is achieved by an initial selection and a proofreading step, mediated by EF-Tu, which forms a ternary complex with aminoacyl(aa)-tRNA. To study the binding modes ...The accuracy of ribosomal translation is achieved by an initial selection and a proofreading step, mediated by EF-Tu, which forms a ternary complex with aminoacyl(aa)-tRNA. To study the binding modes of different aa-tRNAs, we compared cryo-EM maps of the kirromycin-stalled ribosome bound with ternary complexes containing Phe-tRNA(Phe), Trp-tRNA(Trp), or Leu-tRNA(LeuI). The three maps suggest a common binding manner of cognate aa-tRNAs in their specific binding with both the ribosome and EF-Tu. All three aa-tRNAs have the same 'loaded spring' conformation with a kink and twist between the D-stem and anticodon stem. The three complexes are similarly integrated in an interaction network, extending from the anticodon loop through h44 and protein S12 to the EF-Tu-binding CCA end of aa-tRNA, proposed to signal cognate codon-anticodon interaction to the GTPase centre and tune the accuracy of aa-tRNA selection. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 54.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.3 KB 11.3 KB | Display Display | ![]() |
Images | ![]() | 655.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 349.2 KB | Display | ![]() |
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Full document | ![]() | 348.8 KB | Display | |
Data in XML | ![]() | 6.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3eq3MC ![]() 1564C ![]() 3ep2C ![]() 3eq4C 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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Trp-tRNA-EFTu-kir-GDP-70S ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Trp-tRNA-EFTu-GDP-kir-70S ribosome
Entire | Name: Trp-tRNA-EFTu-GDP-kir-70S ribosome |
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Components |
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-Supramolecule #1000: Trp-tRNA-EFTu-GDP-kir-70S ribosome
Supramolecule | Name: Trp-tRNA-EFTu-GDP-kir-70S ribosome / type: sample / ID: 1000 / Oligomeric state: monomeric / Number unique components: 4 |
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Molecular weight | Experimental: 2.8 MDa / Theoretical: 2.8 MDa / Method: sedimentation |
-Supramolecule #1: 70S ribosome
Supramolecule | Name: 70S ribosome / type: complex / ID: 1 / Name.synonym: 70S ribosome / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 2.8 MDa / Theoretical: 2.8 MDa |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.03 mg/mL |
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Buffer | pH: 7.5 Details: HiFi buffer (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, 3.5 mM MgCl2) |
Staining | Type: NEGATIVE / Details: cryo |
Grid | Details: 200 mesh |
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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Temperature | Min: 80.7 K / Max: 80.7 K / Average: 80.7 K |
Alignment procedure | Legacy - Astigmatism: objective corrected at 100,000 times magnification Legacy - Electron beam tilt params: no tilt |
Specialist optics | Energy filter - Name: no energy filter |
Details | automated data collection system AutoEMation (CCD mag. 100000x) |
Date | May 1, 2007 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 25 e/Å2 Details: automated data collection system AutoEMation (CCD mag. 100000x) TVIPS TemCam-F415 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 58269 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder: cartridge / Specimen holder model: OTHER |
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: 9.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Number images used: 290000 |
Final angle assignment | Details: spider |
-Atomic model buiding 1
Initial model | (PDB ID: ![]() 2avy ![]() 2aw4 ![]() 1gix , ) |
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Software | Name: TNT |
Details | Protocol: real space refinement. 1lBM(1989-1996 fragment) |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-3eq3: |