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Yorodumi- EMDB-1076: Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1076 | |||||||||
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Title | Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions. | |||||||||
Map data | This is a volume of 80S ribosome | |||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 15.4 Å | |||||||||
Authors | Spahn CM | |||||||||
Citation | Journal: Cell / Year: 2001 Title: Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions. Authors: C M Spahn / R Beckmann / N Eswar / P A Penczek / A Sali / G Blobel / J Frank / Abstract: A cryo-EM reconstruction of the translating yeast 80S ribosome was analyzed. Computationally separated rRNA and protein densities were used for docking of appropriately modified rRNA models and ...A cryo-EM reconstruction of the translating yeast 80S ribosome was analyzed. Computationally separated rRNA and protein densities were used for docking of appropriately modified rRNA models and homology models of yeast ribosomal proteins. The core of the ribosome shows a remarkable degree of conservation. However, some significant differences in functionally important regions and dramatic changes in the periphery due to expansion segments and additional ribosomal proteins are evident. As in the bacterial ribosome, bridges between the subunits are mainly formed by RNA contacts. Four new bridges are present at the periphery. The position of the P site tRNA coincides precisely with its prokaryotic counterpart, with mainly rRNA contributing to its molecular environment. This analysis presents an exhaustive inventory of an eukaryotic ribosome at the molecular level. | |||||||||
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_1076.map.gz | 7 MB | EMDB map data format | |
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Header (meta data) | emd-1076-v30.xml emd-1076.xml | 8.4 KB 8.4 KB | Display Display | EMDB header |
Images | 1076.gif | 44.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1076 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1076 | HTTPS FTP |
-Validation report
Summary document | emd_1076_validation.pdf.gz | 241.9 KB | Display | EMDB validaton report |
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Full document | emd_1076_full_validation.pdf.gz | 241.1 KB | Display | |
Data in XML | emd_1076_validation.xml.gz | 5.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1076 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1076 | 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_1076.map.gz / Format: CCP4 / Size: 7.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a volume of 80S ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.93 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 : the 80S Ribosome from Saccharomyces cerevisiae
Entire | Name: the 80S Ribosome from Saccharomyces cerevisiae |
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Components |
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-Supramolecule #1000: the 80S Ribosome from Saccharomyces cerevisiae
Supramolecule | Name: the 80S Ribosome from Saccharomyces cerevisiae / type: sample / ID: 1000 / Number unique components: 3 |
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Molecular weight | Theoretical: 3.2 MDa |
-Supramolecule #1: 80S ribosome
Supramolecule | Name: 80S ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Bakers' yeast |
-Macromolecule #1: tRNA
Macromolecule | Name: tRNA / type: rna / ID: 1 / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
-Macromolecule #2: Sec61
Macromolecule | Name: Sec61 / type: protein_or_peptide / ID: 2 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE |
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-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 93 K |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Bits/pixel: 12 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.7 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: defocus group volumes |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER |