+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6044 | |||||||||
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Title | Ribosome conformation along minimum free-energy trajectory | |||||||||
Map data | Conformation of yeast ribosome | |||||||||
Sample |
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Keywords | Translocation / energy landscape / conformations / Brownian machine | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 20.0 Å | |||||||||
Authors | Dashti A / Schwander P / Langlois R / Fung R / Li W / Hosseinizadeh A / Liao HY / Pallesen J / Sharma G / Stupina VA ...Dashti A / Schwander P / Langlois R / Fung R / Li W / Hosseinizadeh A / Liao HY / Pallesen J / Sharma G / Stupina VA / Simon AE / Dinman J / Frank J / Ourmazd A | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2014 Title: Trajectories of the ribosome as a Brownian nanomachine. Authors: Ali Dashti / Peter Schwander / Robert Langlois / Russell Fung / Wen Li / Ahmad Hosseinizadeh / Hstau Y Liao / Jesper Pallesen / Gyanesh Sharma / Vera A Stupina / Anne E Simon / Jonathan D ...Authors: Ali Dashti / Peter Schwander / Robert Langlois / Russell Fung / Wen Li / Ahmad Hosseinizadeh / Hstau Y Liao / Jesper Pallesen / Gyanesh Sharma / Vera A Stupina / Anne E Simon / Jonathan D Dinman / Joachim Frank / Abbas Ourmazd / Abstract: A Brownian machine, a tiny device buffeted by the random motions of molecules in the environment, is capable of exploiting these thermal motions for many of the conformational changes in its work ...A Brownian machine, a tiny device buffeted by the random motions of molecules in the environment, is capable of exploiting these thermal motions for many of the conformational changes in its work cycle. Such machines are now thought to be ubiquitous, with the ribosome, a molecular machine responsible for protein synthesis, increasingly regarded as prototypical. Here we present a new analytical approach capable of determining the free-energy landscape and the continuous trajectories of molecular machines from a large number of snapshots obtained by cryogenic electron microscopy. We demonstrate this approach in the context of experimental cryogenic electron microscope images of a large ensemble of nontranslating ribosomes purified from yeast cells. The free-energy landscape is seen to contain a closed path of low energy, along which the ribosome exhibits conformational changes known to be associated with the elongation cycle. Our approach allows model-free quantitative analysis of the degrees of freedom and the energy landscape underlying continuous conformational changes in nanomachines, including those important for biological function. | |||||||||
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
-Validation report
Summary document | emd_6044_validation.pdf.gz | 78.8 KB | Display | EMDB validaton report |
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Full document | emd_6044_full_validation.pdf.gz | 77.9 KB | Display | |
Data in XML | emd_6044_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6044 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6044 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6044.map.gz / Format: CCP4 / Size: 7.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Conformation of yeast ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
+Supplemental map: emd 6044 additional 1.map
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-Sample components
-Entire : Yeast 80S ribosome
Entire | Name: Yeast 80S ribosome |
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Components |
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-Supramolecule #1000: Yeast 80S ribosome
Supramolecule | Name: Yeast 80S ribosome / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: 80S ribosome
Supramolecule | Name: 80S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Grid | Details: carbon-coated Quantifoil 2/4 grid (Quantifoil Micro Tools GmbH, Jena, Germany) |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK I |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Date | Jan 1, 2010 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal magnification: 80000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Number images used: 849914 |
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