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Yorodumi- EMDB-2847: 2.9A structure of E. coli ribosome-EF-Tu complex by Cs-corrected ... -
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-Basic information
Entry | Database: EMDB / ID: EMD-2847 | |||||||||
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Title | 2.9A structure of E. coli ribosome-EF-Tu complex by Cs-corrected cryo-EM | |||||||||
Map data | Structure of E. coli 70S-EF-Tu-GDP-kirromycin-Phe-tRNAPhe-fMet-tRNAfmet-tRNAfMet complex optimum contour level 0.32-0.64 (1.5-3 sigma) | |||||||||
Sample |
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Keywords | ribosome / translation / protein synthesis / decoding / elongation factor Tu / tRNA / RNA modification / antibiotic | |||||||||
Function / homology | Function and homology information guanyl-nucleotide exchange factor complex / negative regulation of cytoplasmic translational initiation / translational elongation / guanosine tetraphosphate binding / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing ...guanyl-nucleotide exchange factor complex / negative regulation of cytoplasmic translational initiation / translational elongation / guanosine tetraphosphate binding / stringent response / mRNA base-pairing translational repressor activity / 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 / translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / transcription elongation factor complex / response to reactive oxygen species / DNA endonuclease activity / 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 / small ribosomal subunit / cytoplasmic translation / 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 / GTPase activity / negative regulation of DNA-templated transcription / GTP binding / DNA binding / RNA binding / zinc ion binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Fischer N / Neumann P / Konevega AL / Bock LV / Ficner R / Rodnina MV / Stark H | |||||||||
Citation | Journal: Nature / Year: 2015 Title: Structure of the E. coli ribosome-EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM. Authors: Niels Fischer / Piotr Neumann / Andrey L Konevega / Lars V Bock / Ralf Ficner / Marina V Rodnina / Holger Stark / Abstract: Single particle electron cryomicroscopy (cryo-EM) has recently made significant progress in high-resolution structure determination of macromolecular complexes due to improvements in electron ...Single particle electron cryomicroscopy (cryo-EM) has recently made significant progress in high-resolution structure determination of macromolecular complexes due to improvements in electron microscopic instrumentation and computational image analysis. However, cryo-EM structures can be highly non-uniform in local resolution and all structures available to date have been limited to resolutions above 3 Å. Here we present the cryo-EM structure of the 70S ribosome from Escherichia coli in complex with elongation factor Tu, aminoacyl-tRNA and the antibiotic kirromycin at 2.65-2.9 Å resolution using spherical aberration (Cs)-corrected cryo-EM. Overall, the cryo-EM reconstruction at 2.9 Å resolution is comparable to the best-resolved X-ray structure of the E. coli 70S ribosome (2.8 Å), but provides more detailed information (2.65 Å) at the functionally important ribosomal core. The cryo-EM map elucidates for the first time the structure of all 35 rRNA modifications in the bacterial ribosome, explaining their roles in fine-tuning ribosome structure and function and modulating the action of antibiotics. We also obtained atomic models for flexible parts of the ribosome such as ribosomal proteins L9 and L31. The refined cryo-EM-based model presents the currently most complete high-resolution structure of the E. coli ribosome, which demonstrates the power of cryo-EM in structure determination of large and dynamic macromolecular complexes. | |||||||||
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_2847.map.gz | 262.9 MB | EMDB map data format | |
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Header (meta data) | emd-2847-v30.xml emd-2847.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | emd_2847.jpg | 136.4 KB | ||
Others | EMD-2847-FSC-mask.map EMD-2847-full.map EMD-2847-half1.map EMD-2847-half2.map | 282.6 MB 282.6 MB 282.6 MB 282.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2847 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2847 | HTTPS FTP |
-Related structure data
Related structure data | 5afiMC 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_2847.map.gz / Format: CCP4 / Size: 276 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of E. coli 70S-EF-Tu-GDP-kirromycin-Phe-tRNAPhe-fMet-tRNAfmet-tRNAfMet complex optimum contour level 0.32-0.64 (1.5-3 sigma) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.75525 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Supplemental map: EMD-2847-FSC-mask.map
File | EMD-2847-FSC-mask.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: EMD-2847-full.map
File | EMD-2847-full.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: EMD-2847-half1.map
File | EMD-2847-half1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: EMD-2847-half2.map
File | EMD-2847-half2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : E. coli 70S-EF-Tu-GDP-kirromycin-Phe-tRNAPhe-fMet-tRNAfmet-tRNAfM...
Entire | Name: E. coli 70S-EF-Tu-GDP-kirromycin-Phe-tRNAPhe-fMet-tRNAfmet-tRNAfMet complex |
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Components |
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-Supramolecule #1000: E. coli 70S-EF-Tu-GDP-kirromycin-Phe-tRNAPhe-fMet-tRNAfmet-tRNAfM...
Supramolecule | Name: E. coli 70S-EF-Tu-GDP-kirromycin-Phe-tRNAPhe-fMet-tRNAfmet-tRNAfMet complex type: sample / ID: 1000 / Number unique components: 6 |
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Molecular weight | Theoretical: 2.8 MDa |
-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: Escherichia coli (E. coli) |
-Macromolecule #1: elongation factor Tu
Macromolecule | Name: elongation factor Tu / type: protein_or_peptide / ID: 1 / Name.synonym: EF-Tu Details: EF-Tu-GDP stalled on the ribosome by the antibiotic kirromycin Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #2: Phe-tRNAPhe
Macromolecule | Name: Phe-tRNAPhe / type: rna / ID: 2 / Classification: TRANSFER / Structure: OTHER / Synthetic?: No |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #3: initiator fMet-tRNAfMet
Macromolecule | Name: initiator fMet-tRNAfMet / type: rna / ID: 3 / Classification: TRANSFER / Structure: OTHER / Synthetic?: No |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #4: deacylated tRNAfMet
Macromolecule | Name: deacylated tRNAfMet / type: rna / ID: 4 / Classification: TRANSFER / Structure: OTHER / Synthetic?: No |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #5: mRNA
Macromolecule | Name: mRNA / type: rna / ID: 5 / Classification: TRANSFER / Structure: SINGLE STRANDED / Synthetic?: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Sequence | String: GGCAAGGAGG UAAAUAAUGU UCGUUACGAC |
-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: 50mM Hepes-KOH, 70mM NH4Cl, 30mM KCl, 20mM MgCl2, 1mM DTT, 0.6mM spermine, 0.4mM spermidine, 0.15mM kirromycin |
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Grid | Details: Quantifoil grids (3.5/1um) covered with pre-floated continuous carbon |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: OTHER |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 192000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Alignment procedure | Legacy - Astigmatism: Using a Cs-corrector from CEOS electron optical aberrations were corrected to residual phase errors of 45degree at scattering angles of >12 to 15 mrad. |
Date | Dec 20, 2011 |
Image recording | Category: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Number real images: 24684 / Average electron dose: 40 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: local CTF correction |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: OTHER / Software - Name: custom-made, IMAGIC-5, Relion, 1.2 / Number images used: 417201 |