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Yorodumi- EMDB-1395: Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1395 | |||||||||
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Title | Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. | |||||||||
Map data | Cryo-EM map of E.coli 70S ribosome | |||||||||
Sample |
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Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.8 Å | |||||||||
Authors | Valle M / Zavialov A / Li W / Stagg SM / Sengupta J / Nielsen RC / Nissen P / Harvey SC / Ehrenberg M / Frank J | |||||||||
Citation | Journal: Nat Struct Biol / Year: 2003 Title: Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Authors: Mikel Valle / Andrey Zavialov / Wen Li / Scott M Stagg / Jayati Sengupta / Rikke C Nielsen / Poul Nissen / Stephen C Harvey / Måns Ehrenberg / Joachim Frank / Abstract: Aminoacyl-tRNAs (aa-tRNAs) are delivered to the ribosome as part of the ternary complex of aa-tRNA, elongation factor Tu (EF-Tu) and GTP. Here, we present a cryo-electron microscopy (cryo-EM) study, ...Aminoacyl-tRNAs (aa-tRNAs) are delivered to the ribosome as part of the ternary complex of aa-tRNA, elongation factor Tu (EF-Tu) and GTP. Here, we present a cryo-electron microscopy (cryo-EM) study, at a resolution of approximately 9 A, showing that during the incorporation of the aa-tRNA into the 70S ribosome of Escherichia coli, the flexibility of aa-tRNA allows the initial codon recognition and its accommodation into the ribosomal A site. In addition, a conformational change observed in the GTPase-associated center (GAC) of the ribosomal 50S subunit may provide the mechanism by which the ribosome promotes a relative movement of the aa-tRNA with respect to EF-Tu. This relative rearrangement seems to facilitate codon recognition by the incoming aa-tRNA, and to provide the codon-anticodon recognition-dependent signal for the GTPase activity of EF-Tu. From these new findings we propose a mechanism that can explain the sequence of events during the decoding of mRNA on the ribosome. | |||||||||
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_1395.map.gz | 7.9 MB | EMDB map data format | |
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Header (meta data) | emd-1395-v30.xml emd-1395.xml | 8.7 KB 8.7 KB | Display Display | EMDB header |
Images | 1395.gif | 38.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1395 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1395 | HTTPS FTP |
-Validation report
Summary document | emd_1395_validation.pdf.gz | 241.1 KB | Display | EMDB validaton report |
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Full document | emd_1395_full_validation.pdf.gz | 240.2 KB | Display | |
Data in XML | emd_1395_validation.xml.gz | 6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1395 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1395 | HTTPS FTP |
-Related structure data
Related structure data | 1055C 1056C 1qzaC 1qzbC 1qzcC 1qzdC 1r2wC 1r2xC 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_1395.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of E.coli 70S ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.82 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 : 70S Post-initiation complex with fMettRNAfMet
Entire | Name: 70S Post-initiation complex with fMettRNAfMet |
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Components |
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-Supramolecule #1000: 70S Post-initiation complex with fMettRNAfMet
Supramolecule | Name: 70S Post-initiation complex with fMettRNAfMet / type: sample / ID: 1000 / Number unique components: 3 |
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-Supramolecule #1: Post-initiation Complex
Supramolecule | Name: Post-initiation Complex / type: complex / ID: 1 / Ribosome-details: ribosome-prokaryote: ALL |
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-Macromolecule #1: tRNA
Macromolecule | Name: tRNA / type: rna / ID: 1 / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #2: mRNA
Macromolecule | Name: mRNA / type: rna / ID: 2 / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Details: Rapid-freezing in liquid ethane |
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-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 93 K |
Alignment procedure | Legacy - Electron beam tilt params: 0 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 49650 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: cryo transfer / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: CTF correctionn of 3D map |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER package |