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Yorodumi- EMDB-5267: Intermediate states observed in the pre-translocation ribosome du... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5267 | |||||||||
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Title | Intermediate states observed in the pre-translocation ribosome during tRNA translocation | |||||||||
Map data | E. coli ribosome: intermediate rotated structure 2 | |||||||||
Sample |
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Keywords | ribosome / translocation / tRNA | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.2 Å | |||||||||
Authors | Fu J / Munro J / Blanchard SC / Frank J | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2011 Title: Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation. Authors: Jie Fu / James B Munro / Scott C Blanchard / Joachim Frank / Abstract: mRNA-tRNA translocation is a central and highly regulated process during translational elongation. Along with the mRNA, tRNA moves through the ribosome in a stepwise fashion. Using cryoelectron ...mRNA-tRNA translocation is a central and highly regulated process during translational elongation. Along with the mRNA, tRNA moves through the ribosome in a stepwise fashion. Using cryoelectron microscopy on ribosomes with a P-loop mutation, we have identified novel structural intermediates likely to exist transiently during translocation. Our observations suggest a mechanism by which the rate of translocation can be regulated. | |||||||||
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_5267.map.gz | 1.2 MB | EMDB map data format | |
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Header (meta data) | emd-5267-v30.xml emd-5267.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
Images | emd_5267_1.jpg | 153.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5267 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5267 | HTTPS FTP |
-Validation report
Summary document | emd_5267_validation.pdf.gz | 77.6 KB | Display | EMDB validaton report |
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Full document | emd_5267_full_validation.pdf.gz | 76.7 KB | Display | |
Data in XML | emd_5267_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5267 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5267 | HTTPS FTP |
-Related 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_5267.map.gz / Format: CCP4 / Size: 7.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | E. coli ribosome: intermediate rotated structure 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3 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 : pre-translocation ribosome complex
Entire | Name: pre-translocation ribosome complex |
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Components |
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-Supramolecule #1000: pre-translocation ribosome complex
Supramolecule | Name: pre-translocation ribosome complex / type: sample / ID: 1000 / Number unique components: 3 |
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Molecular weight | Theoretical: 2.5 MDa |
-Supramolecule #1: ribosome
Supramolecule | Name: ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 2.5 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: vitrobot / Method: blot for 8 seconds |
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-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Average: 82 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 24 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 100000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder: cartridge / Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: defocus group and wiener filter |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 84000 |
Final two d classification | Number classes: 4 |