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- EMDB-3118: Cryo-tomogram of the [PSI+] prion assembly in a vitrified cryosec... -

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Basic information

Entry
Database: EMDB / ID: EMD-3118
TitleCryo-tomogram of the [PSI+] prion assembly in a vitrified cryosection of a Hsp70 deletion mutant yeast cell.
Map dataCryo-tomogram of a vitrified yeast cryosection
Sample
  • Sample: Vitreous cryosection of a Hsp70 (Ssa1) deletion mutant yeast cell
  • Organelle or cellular component: Yeast Prion aggregate deposit
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodelectron tomography / cryo EM
AuthorsO'Driscoll J / Clare D / Saibil H
CitationJournal: J Cell Biol / Year: 2015
Title: Prion aggregate structure in yeast cells is determined by the Hsp104-Hsp110 disaggregase machinery.
Authors: Jonathan O'Driscoll / Daniel Clare / Helen Saibil /
Abstract: Prions consist of misfolded proteins that have adopted an infectious amyloid conformation. In vivo, prion biogenesis is intimately associated with the protein quality control machinery. Using ...Prions consist of misfolded proteins that have adopted an infectious amyloid conformation. In vivo, prion biogenesis is intimately associated with the protein quality control machinery. Using electron tomography, we probed the effects of the heat shock protein Hsp70 chaperone system on the structure of a model yeast [PSI+] prion in situ. Individual Hsp70 deletions shift the balance between fibril assembly and disassembly, resulting in a variable shell of nonfibrillar, but still immobile, aggregates at the surface of the [PSI+] prion deposits. Both Hsp104 (an Hsp100 disaggregase) and Sse1 (the major yeast form of Hsp110) were localized to this surface shell of [PSI+] deposits in the deletion mutants. Elevation of Hsp104 expression promoted the appearance of this novel, nonfibrillar form of the prion aggregate. Moreover, Sse1 was found to regulate prion fibril length. Our studies reveal a key role for Sse1 (Hsp110), in cooperation with Hsp104, in regulating the length and assembly state of [PSI+] prion fibrils in vivo.
History
DepositionAug 10, 2015-
Header (metadata) releaseSep 16, 2015-
Map releaseDec 30, 2015-
UpdateMar 9, 2016-
Current statusMar 9, 2016Processing site: PDBe / Status: Released

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Structure visualization

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Supplemental images

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Map

FileDownload / File: emd_3118.map.gz / Format: CCP4 / Size: 172.7 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationCryo-tomogram of a vitrified yeast cryosection
Voxel sizeX=Y=Z: 11.26 Å
Density
Minimum - Maximum-110.0 - 116.0
Average (Standard dev.)-1.66636431 (±11.69381237)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-43
Dimensions1806201351
Spacing1806201351
CellA: 22666.38 Å / B: 20335.56 Å / C: 574.26 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z11.26000049677111.2600005537111.26
M x/y/z2013180651
origin x/y/z0.0000.0000.000
length x/y/z22666.38120335.561574.260
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS00-43
NC/NR/NS2013180651
D min/max/mean-110.000116.000-1.666

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Supplemental data

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Sample components

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Entire : Vitreous cryosection of a Hsp70 (Ssa1) deletion mutant yeast cell

EntireName: Vitreous cryosection of a Hsp70 (Ssa1) deletion mutant yeast cell
Components
  • Sample: Vitreous cryosection of a Hsp70 (Ssa1) deletion mutant yeast cell
  • Organelle or cellular component: Yeast Prion aggregate deposit

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Supramolecule #1000: Vitreous cryosection of a Hsp70 (Ssa1) deletion mutant yeast cell

SupramoleculeName: Vitreous cryosection of a Hsp70 (Ssa1) deletion mutant yeast cell
type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Yeast Prion aggregate deposit

SupramoleculeName: Yeast Prion aggregate deposit / type: organelle_or_cellular_component / ID: 1 / Name.synonym: [PSI+] / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: 74D-694 / synonym: Yeast / Location in cell: cytosol

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4 / Details: 50 mM Tris
GridDetails: 200 mesh c-flat carbon support film with an additional 5 nm thin continuous
VitrificationCryogen name: OTHER / Chamber temperature: 78 K / Instrument: OTHER

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.3 mm / Nominal defocus max: 10.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 20000
Sample stageSpecimen holder: Liquid nitrogen cooled / Specimen holder model: OTHER / Tilt series - Axis1 - Min angle: -56 ° / Tilt series - Axis1 - Max angle: 55 ° / Tilt series - Axis1 - Angle increment: 1.5 °
TemperatureMin: 76 K / Max: 78 K / Average: 77 K
DateJun 21, 2013
Image recordingCategory: CCD / Film or detector model: GATAN MULTISCAN / Number real images: 75 / Average electron dose: 1 e/Å2
Details: Each image was binned by 2 from the original image stack collected on the CCD camera
Bits/pixel: 8
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 75
DetailsReconstructed using IMOD, no CTF correction was performed. The reconstruction was NAD filtered.

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