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- EMDB-5267: Intermediate states observed in the pre-translocation ribosome du... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5267 | |||||||||
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Title | Intermediate states observed in the pre-translocation ribosome during tRNA translocation | |||||||||
![]() | E. coli ribosome: intermediate rotated structure 2 | |||||||||
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![]() | ribosome / translocation / tRNA | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.2 Å | |||||||||
![]() | Fu J / Munro J / Blanchard SC / Frank J | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 8.5 KB 8.5 KB | Display Display | ![]() |
Images | ![]() | 153.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 77.6 KB | Display | ![]() |
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Full document | ![]() | 76.7 KB | Display | |
Data in XML | ![]() | 493 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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 | 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
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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: ![]() ![]() |
Molecular weight | Theoretical: 2.5 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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: ![]() |
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 |
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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 |