[English] 日本語
Yorodumi
- EMDB-11416: Tomogram of GFP-a-synuclein inclusion in primary mouse neuron exp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11416
TitleTomogram of GFP-a-synuclein inclusion in primary mouse neuron expressing GFP-a-synuclein, seeded with MSA aggregates
Map dataTomogram of GFP-a-synuclein inclusion in primary mouse neurons seeded with MSA aggregates
Sample
  • Cell: Tomogram of GFP-a-synuclein inclusion in primary mouse neuron expressing GFP-a-synuclein, seeded with MSA aggregates
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsTrinkaus VA / Hartl FU / Fernandez-Busnadiego R
Funding support Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)FP7 GA ERC-2012-SyG_318987-ToPAG Germany
German Research Foundation (DFG)EXC 2067/1- 390729940 Germany
CitationJournal: Nat Commun / Year: 2021
Title: In situ architecture of neuronal α-Synuclein inclusions.
Authors: Victoria A Trinkaus / Irene Riera-Tur / Antonio Martínez-Sánchez / Felix J B Bäuerlein / Qiang Guo / Thomas Arzberger / Wolfgang Baumeister / Irina Dudanova / Mark S Hipp / F Ulrich Hartl ...Authors: Victoria A Trinkaus / Irene Riera-Tur / Antonio Martínez-Sánchez / Felix J B Bäuerlein / Qiang Guo / Thomas Arzberger / Wolfgang Baumeister / Irina Dudanova / Mark S Hipp / F Ulrich Hartl / Rubén Fernández-Busnadiego /
Abstract: The molecular architecture of α-Synuclein (α-Syn) inclusions, pathognomonic of various neurodegenerative disorders, remains unclear. α-Syn inclusions were long thought to consist mainly of α-Syn ...The molecular architecture of α-Synuclein (α-Syn) inclusions, pathognomonic of various neurodegenerative disorders, remains unclear. α-Syn inclusions were long thought to consist mainly of α-Syn fibrils, but recent reports pointed to intracellular membranes as the major inclusion component. Here, we use cryo-electron tomography (cryo-ET) to image neuronal α-Syn inclusions in situ at molecular resolution. We show that inclusions seeded by α-Syn aggregates produced recombinantly or purified from patient brain consist of α-Syn fibrils crisscrossing a variety of cellular organelles. Using gold-labeled seeds, we find that aggregate seeding is predominantly mediated by small α-Syn fibrils, from which cytoplasmic fibrils grow unidirectionally. Detailed analysis of membrane interactions revealed that α-Syn fibrils do not contact membranes directly, and that α-Syn does not drive membrane clustering. Altogether, we conclusively demonstrate that neuronal α-Syn inclusions consist of α-Syn fibrils intermixed with membranous organelles, and illuminate the mechanism of aggregate seeding and cellular interaction.
History
DepositionJul 17, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateAug 4, 2021-
Current statusAug 4, 2021Processing 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
Supplemental images

emd_11416.png

Downloads & links

-
Map

FileDownload / File: emd_11416.map.gz / Format: CCP4 / Size: 778.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram of GFP-a-synuclein inclusion in primary mouse neurons seeded with MSA aggregates
Voxel sizeX=Y=Z: 14.08 Å
Density
Minimum - Maximum-6049.4873 - 3091.287
Average (Standard dev.)58.820164 (±170.25024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-119
Dimensions928928237
Spacing928928237
CellA: 13066.24 Å / B: 13066.24 Å / C: 3336.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z14.0814.0814.08
M x/y/z928928237
origin x/y/z0.0000.0000.000
length x/y/z13066.24013066.2403336.960
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS00-119
NC/NR/NS928928237
D min/max/mean-6049.4873091.28758.820

-
Supplemental data

-
Sample components

-
Entire : Tomogram of GFP-a-synuclein inclusion in primary mouse neuron exp...

EntireName: Tomogram of GFP-a-synuclein inclusion in primary mouse neuron expressing GFP-a-synuclein, seeded with MSA aggregates
Components
  • Cell: Tomogram of GFP-a-synuclein inclusion in primary mouse neuron expressing GFP-a-synuclein, seeded with MSA aggregates

-
Supramolecule #1: Tomogram of GFP-a-synuclein inclusion in primary mouse neuron exp...

SupramoleculeName: Tomogram of GFP-a-synuclein inclusion in primary mouse neuron expressing GFP-a-synuclein, seeded with MSA aggregates
type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/4 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 80 % / Chamber temperature: 310 K / Instrument: FEI VITROBOT MARK IV
Cryo protectant10 % Glycerol
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.1 nA / Focused ion beam - Duration: 2400 sec. / Focused ion beam - Temperature: 77 K / Focused ion beam - Initial thickness: 1000 nm / Focused ion beam - Final thickness: 150 nm
Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Quanta FIB. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 7.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 42000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 70.0 K / Max: 75.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 14-20 / Number grids imaged: 1 / Number real images: 50 / Average exposure time: 4.0 sec. / Average electron dose: 2.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionSoftware - Name: IMOD (ver. 4.9.0) / Number images used: 50

+
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