[English] 日本語
Yorodumi
- EMDB-3124: Cryo-tomogram of an isolated fibrillar [PSI+] prion assembly -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3124
TitleCryo-tomogram of an isolated fibrillar [PSI+] prion assembly
Map dataReconstruction of an isolated amyloid assembly
Sample
  • Sample: Isolated yeast prion fibril assembly
  • 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 11, 2015-
Header (metadata) releaseDec 30, 2015-
Map releaseDec 30, 2015-
UpdateJan 13, 2016-
Current statusJan 13, 2016Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3124.tif

Downloads & links

-
Map

FileDownload / File: emd_3124.map.gz / Format: CCP4 / Size: 424.9 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationReconstruction of an isolated amyloid assembly
Voxel sizeX=Y=Z: 11.41 Å
Density
Minimum - Maximum-119.0 - 47.0
Average (Standard dev.)-2.54386663 (±3.8979497)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin0-39221
Dimensions18811650147
Spacing18811650147
CellA: 18826.5 Å / B: 21462.209 Å / C: 1677.27 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z11.4111.40999946836811.41
M x/y/z16501881147
origin x/y/z0.0000.0000.000
length x/y/z18826.50021462.2091677.270
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-392021
NC/NR/NS16501881147
D min/max/mean-119.00047.000-2.544

-
Supplemental data

-
Sample components

-
Entire : Isolated yeast prion fibril assembly

EntireName: Isolated yeast prion fibril assembly
Components
  • Sample: Isolated yeast prion fibril assembly
  • Organelle or cellular component: Yeast Prion aggregate deposit

-
Supramolecule #1000: Isolated yeast prion fibril assembly

SupramoleculeName: Isolated yeast prion fibril assembly / type: sample / ID: 1000 / Number unique components: 1

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.4 / Details: 50 mM Tris
GridDetails: 200 mesh c-flat carbon support film augmented with an additional 5 nm thin continuous carbon film
VitrificationCryogen name: ETHANE / Chamber temperature: 78 K / Instrument: HOMEMADE PLUNGER / Method: Blot for 8 seconds before plunging

-
Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 76 K / Max: 78 K / Average: 77 K
DateJun 21, 2013
Image recordingCategory: CCD / Film or detector model: GATAN MULTISCAN / Number real images: 81 / 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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: -60 ° / Tilt series - Axis1 - Max angle: 60 ° / Tilt series - Axis1 - Angle increment: 1.5 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

DetailsReconstructed using IMOD, no CTF correction was performed. The final reconstruction was binned by 2. The reconstruction was NAD filtered.
Final reconstructionSoftware - Name: IMOD / Number images used: 75

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more