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Yorodumi- EMDB-15215: Asymmetric reconstruction of averaged ribosomes from Saccharomyce... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15215 | ||||||||||||||||||
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Title | Asymmetric reconstruction of averaged ribosomes from Saccharomyces cerevisiae | ||||||||||||||||||
Map data | Asymmetric reconstruction of averaged ribosomes from Saccharomyces cerevisiae | ||||||||||||||||||
Sample |
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Keywords | ribosome / replication / active translation / ribosomal states / polysomes | ||||||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.1 Å | ||||||||||||||||||
Authors | Schmidt L / Tueting C / Kyrilis F / Hamdi F / Semchonok DA / Kastritis PL | ||||||||||||||||||
Funding support | Germany, European Union, 5 items
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Citation | Journal: Commun Biol / Year: 2024 Title: Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts. Authors: Lisa Schmidt / Christian Tüting / Fotis L Kyrilis / Farzad Hamdi / Dmitry A Semchonok / Gerd Hause / Annette Meister / Christian Ihling / Milton T Stubbs / Andrea Sinz / Panagiotis L Kastritis / Abstract: The high abundance of most viruses in infected host cells benefits their structural characterization. However, endogenous viruses are present in low copy numbers and are therefore challenging to ...The high abundance of most viruses in infected host cells benefits their structural characterization. However, endogenous viruses are present in low copy numbers and are therefore challenging to investigate. Here, we retrieve cell extracts enriched with an endogenous virus, the yeast L-A virus. The determined cryo-EM structure discloses capsid-stabilizing cation-π stacking, widespread across viruses and within the Totiviridae, and an interplay of non-covalent interactions from ten distinct capsomere interfaces. The capsid-embedded mRNA decapping active site trench is supported by a constricting movement of two flexible opposite-facing loops. tRNA-loaded polysomes and other biomacromolecules, presumably mRNA, are found in virus proximity within the cell extract. Mature viruses participate in larger viral communities resembling their rare in-cell equivalents in terms of size, composition, and inter-virus distances. Our results collectively describe a 3D-architecture of a viral milieu, opening the door to cell-extract-based high-resolution structural virology. #1: Journal: Biorxiv / Year: 2022 Title: Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts Authors: Schmidt L / Tuting C / Kyrilis FL / Hamdi F / Semchonok DA / Hause G / Meister A / Ihling C / Shah PNM / Stubbs MT / Sinz A / Stuart DI / Kastritis PL | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15215.map.gz | 7.5 MB | EMDB map data format | |
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Header (meta data) | emd-15215-v30.xml emd-15215.xml | 31.5 KB 31.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15215_fsc.xml | 5.9 KB | Display | FSC data file |
Images | emd_15215.png | 182.7 KB | ||
Filedesc metadata | emd-15215.cif.gz | 5.1 KB | ||
Others | emd_15215_additional_1.map.gz emd_15215_additional_2.map.gz emd_15215_additional_3.map.gz emd_15215_additional_4.map.gz emd_15215_additional_5.map.gz emd_15215_additional_6.map.gz emd_15215_half_map_1.map.gz emd_15215_half_map_2.map.gz | 7.5 MB 7.5 MB 7.5 MB 7.5 MB 7.5 MB 7.5 MB 7.3 MB 7.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15215 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15215 | HTTPS FTP |
-Validation report
Summary document | emd_15215_validation.pdf.gz | 701.1 KB | Display | EMDB validaton report |
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Full document | emd_15215_full_validation.pdf.gz | 700.7 KB | Display | |
Data in XML | emd_15215_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | emd_15215_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15215 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15215 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15215.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Asymmetric reconstruction of averaged ribosomes from Saccharomyces cerevisiae | ||||||||||||||||||||
Voxel size | X=Y=Z: 3.177 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Reconstructed map of a ribosome after variability analysis...
File | emd_15215_additional_1.map | ||||||||||||
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Annotation | Reconstructed map of a ribosome after variability analysis showing tRNA occupation at sites A/A P/P | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Reconstructed map of a ribosome after variability analysis...
File | emd_15215_additional_2.map | ||||||||||||
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Annotation | Reconstructed map of a ribosome after variability analysis showing tRNA occupation at sites P/P E/E | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Reconstructed map of a ribosome after variability analysis...
File | emd_15215_additional_3.map | ||||||||||||
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Annotation | Reconstructed map of a ribosome after variability analysis showing tRNA occupation at sites P/E E/- | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Reconstructed map of a ribosome after variability analysis...
File | emd_15215_additional_4.map | ||||||||||||
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Annotation | Reconstructed map of a ribosome after variability analysis showing tRNA occupation at sites A/P P/E | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Reconstructed map of a ribosome after variability analysis...
File | emd_15215_additional_5.map | ||||||||||||
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Annotation | Reconstructed map of a ribosome after variability analysis showing tRNA occupation at site A/P | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Reconstructed map of a ribosome after variability analysis...
File | emd_15215_additional_6.map | ||||||||||||
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Annotation | Reconstructed map of a ribosome after variability analysis showing tRNA occupation at site A/A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Asymmetric reconstruction of averaged ribosomes from Saccharomyces cerevisiae...
File | emd_15215_half_map_1.map | ||||||||||||
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Annotation | Asymmetric reconstruction of averaged ribosomes from Saccharomyces cerevisiae - Half Map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Asymmetric reconstruction of averaged ribosomes from Saccharomyces cerevisiae...
File | emd_15215_half_map_2.map | ||||||||||||
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Annotation | Asymmetric reconstruction of averaged ribosomes from Saccharomyces cerevisiae - Half Map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Saccharomyces cerevisiae ribosomes
Entire | Name: Saccharomyces cerevisiae ribosomes |
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Components |
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-Supramolecule #1: Saccharomyces cerevisiae ribosomes
Supramolecule | Name: Saccharomyces cerevisiae ribosomes / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | 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
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.4 / Component - Concentration: 200.0 mM / Component - Formula: CH3COONH4 / Component - Name: Ammoniumacetate Details: pH of the buffer was adjusted with NaOH buffer was filtered and sonicated |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.04 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 2 and blot time 6 before plunging. |
Details | heterogenous cell extract |
-Electron microscopy
Microscope | TFS GLACIOS |
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Temperature | Min: 77.0 K / Max: 118.0 K |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 7 / Number real images: 2728 / Average exposure time: 3.61 sec. / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 44067 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 45000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |