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Yorodumi- EMDB-2103: Heritable yeast prions have a highly organized 3-dimensional arch... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2103 | |||||||||
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Title | Heritable yeast prions have a highly organized 3-dimensional architecture with inter-fiber structures | |||||||||
Map data | sub-tomogram average | |||||||||
Sample |
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Keywords | amyloid fibrils / cryo-electron tomography / sub-tomogram averaging / yeast prions | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | subtomogram averaging / cryo EM | |||||||||
Authors | Frangakis A / Saibil HR | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2012 Title: Heritable yeast prions have a highly organized three-dimensional architecture with interfiber structures. Authors: Helen R Saibil / Anja Seybert / Anja Habermann / Juliane Winkler / Mikhail Eltsov / Mario Perkovic / Daniel Castaño-Diez / Margot P Scheffer / Uta Haselmann / Petr Chlanda / Susan Lindquist ...Authors: Helen R Saibil / Anja Seybert / Anja Habermann / Juliane Winkler / Mikhail Eltsov / Mario Perkovic / Daniel Castaño-Diez / Margot P Scheffer / Uta Haselmann / Petr Chlanda / Susan Lindquist / Jens Tyedmers / Achilleas S Frangakis / Abstract: Yeast prions constitute a "protein-only" mechanism of inheritance that is widely deployed by wild yeast to create diverse phenotypes. One of the best-characterized prions, [PSI(+)], is governed by a ...Yeast prions constitute a "protein-only" mechanism of inheritance that is widely deployed by wild yeast to create diverse phenotypes. One of the best-characterized prions, [PSI(+)], is governed by a conformational change in the prion domain of Sup35, a translation-termination factor. When this domain switches from its normal soluble form to an insoluble amyloid, the ensuing change in protein synthesis creates new traits. Two factors make these traits heritable: (i) the amyloid conformation is self-templating; and (ii) the protein-remodeling factor heat-shock protein (Hsp)104 (acting together with Hsp70 chaperones) partitions the template to daughter cells with high fidelity. Prions formed by several other yeast proteins create their own phenotypes but share the same mechanistic basis of inheritance. Except for the amyloid fibril itself, the cellular architecture underlying these protein-based elements of inheritance is unknown. To study the 3D arrangement of prion assemblies in their cellular context, we examined yeast [PSI(+)] prions in the native, hydrated state in situ, taking advantage of recently developed methods for cryosectioning of vitrified cells. Cryo-electron tomography of the vitrified sections revealed the prion assemblies as aligned bundles of regularly spaced fibrils in the cytoplasm with no bounding structures. Although the fibers were widely spaced, other cellular complexes, such as ribosomes, were excluded from the fibril arrays. Subtomogram image averaging, made possible by the organized nature of the assemblies, uncovered the presence of an additional array of densities between the fibers. We suggest these structures constitute a self-organizing mechanism that coordinates fiber deposition and the regulation of prion inheritance. | |||||||||
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_2103.map.gz | 1.1 MB | EMDB map data format | |
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Header (meta data) | emd-2103-v30.xml emd-2103.xml | 7.1 KB 7.1 KB | Display Display | EMDB header |
Images | emd_2103.png | 116.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2103 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2103 | HTTPS FTP |
-Validation report
Summary document | emd_2103_validation.pdf.gz | 199.5 KB | Display | EMDB validaton report |
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Full document | emd_2103_full_validation.pdf.gz | 198.6 KB | Display | |
Data in XML | emd_2103_validation.xml.gz | 3.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2103 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2103 | 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_2103.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | sub-tomogram average | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6 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 : Yeast Prions
Entire | Name: Yeast Prions |
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Components |
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-Supramolecule #1000: Yeast Prions
Supramolecule | Name: Yeast Prions / type: sample / ID: 1000 Details: 200 nm thick vitreous sections of yeast s. cerevissae. Number unique components: 1 |
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-Supramolecule #1: Prion
Supramolecule | Name: Prion / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Bakers yeast |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: OTHER |
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-Electron microscopy
Microscope | FEI POLARA 300 |
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Date | Dec 9, 2007 |
Image recording | Digitization - Scanner: OTHER |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | Average number of projections used in the 3D reconstructions: 400. |
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