[English] 日本語
Yorodumi
- EMDB-12539: Tomogram of mutant huntingtin containing organelle resembles auto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12539
TitleTomogram of mutant huntingtin containing organelle resembles autolysosome/residual body in 6-month-old zQ175 mice
Map dataTomogram of mutant HTT containing organelle resembles autolysosome/residual body in 6-month-old zQ175 mice.
Sample
  • Tissue: Mutant huntingtin containing organelle in hippocampal CA1 neuron from zQ175 knock-in mice.
Biological speciesMus musculus (house mouse)
Methodelectron tomography / negative staining
AuthorsZhou Y / Saibil HR
Funding support United Kingdom, United States, 4 items
OrganizationGrant numberCountry
Wellcome Trust106249/Z/14/Z United Kingdom
Wellcome Trust079605/2/06/2 United Kingdom
The CHDI Foundation United States
UK Dementia Research Institute United Kingdom
CitationJournal: Acta Neuropathol Commun / Year: 2021
Title: Correlative light and electron microscopy suggests that mutant huntingtin dysregulates the endolysosomal pathway in presymptomatic Huntington's disease.
Authors: Ya Zhou / Thomas R Peskett / Christian Landles / John B Warner / Kirupa Sathasivam / Edward J Smith / Shu Chen / Ronald Wetzel / Hilal A Lashuel / Gillian P Bates / Helen R Saibil /
Abstract: Huntington's disease (HD) is a late onset, inherited neurodegenerative disorder for which early pathogenic events remain poorly understood. Here we show that mutant exon 1 HTT proteins are recruited ...Huntington's disease (HD) is a late onset, inherited neurodegenerative disorder for which early pathogenic events remain poorly understood. Here we show that mutant exon 1 HTT proteins are recruited to a subset of cytoplasmic aggregates in the cell bodies of neurons in brain sections from presymptomatic HD, but not wild-type, mice. This occurred in a disease stage and polyglutamine-length dependent manner. We successfully adapted a high-resolution correlative light and electron microscopy methodology, originally developed for mammalian and yeast cells, to allow us to correlate light microscopy and electron microscopy images on the same brain section within an accuracy of 100 nm. Using this approach, we identified these recruitment sites as single membrane bound, vesicle-rich endolysosomal organelles, specifically as (1) multivesicular bodies (MVBs), or amphisomes and (2) autolysosomes or residual bodies. The organelles were often found in close-proximity to phagophore-like structures. Immunogold labeling localized mutant HTT to non-fibrillar, electron lucent structures within the lumen of these organelles. In presymptomatic HD, the recruitment organelles were predominantly MVBs/amphisomes, whereas in late-stage HD, there were more autolysosomes or residual bodies. Electron tomograms indicated the fusion of small vesicles with the vacuole within the lumen, suggesting that MVBs develop into residual bodies. We found that markers of MVB-related exocytosis were depleted in presymptomatic mice and throughout the disease course. This suggests that endolysosomal homeostasis has moved away from exocytosis toward lysosome fusion and degradation, in response to the need to clear the chronically aggregating mutant HTT protein, and that this occurs at an early stage in HD pathogenesis.
History
DepositionMar 3, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateMay 5, 2021-
Current statusMay 5, 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_12539.png

Downloads & links

-
Map

FileDownload / File: emd_12539.map.gz / Format: CCP4 / Size: 4.7 GB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationTomogram of mutant HTT containing organelle resembles autolysosome/residual body in 6-month-old zQ175 mice.
Voxel sizeX=Y=Z: 4.441 Å
Density
Minimum - Maximum-82.0 - 87.0
Average (Standard dev.)-7.173655 (±10.642627)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-26-3552
Dimensions36163131446
Spacing31313616446
CellA: 13904.7705 Å / B: 16058.656 Å / C: 1980.686 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z4.4414.4414.441
M x/y/z31313616446
origin x/y/z0.0000.0000.000
length x/y/z13904.77116058.6561980.686
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-35-2652
NC/NR/NS31313616446
D min/max/mean-82.00087.000-7.174

-
Supplemental data

-
Sample components

-
Entire : Mutant huntingtin containing organelle in hippocampal CA1 neuron ...

EntireName: Mutant huntingtin containing organelle in hippocampal CA1 neuron from zQ175 knock-in mice.
Components
  • Tissue: Mutant huntingtin containing organelle in hippocampal CA1 neuron from zQ175 knock-in mice.

-
Supramolecule #1: Mutant huntingtin containing organelle in hippocampal CA1 neuron ...

SupramoleculeName: Mutant huntingtin containing organelle in hippocampal CA1 neuron from zQ175 knock-in mice.
type: tissue / ID: 1 / Parent: 0
Details: Cytoplasmic inclusion sites identified by correlative fluorescence/EM on freeze substituted brain sections.
Source (natural)Organism: Mus musculus (house mouse) / Strain: C57BL/6J / Organ: Brain / Tissue: hippocampus CA1

-
Experimental details

-
Structure determination

Methodnegative staining
Processingelectron tomography
Aggregation statetissue

-
Sample preparation

BufferpH: 7 / Details: MilliQ water was used.
StainingType: NEGATIVE / Material: Uranyl acetate
Sugar embeddingMaterial: Lowicryl HM20
Details: High pressure frozen samples were freeze substituted in a Leica AFS
DetailsBrain slices were high pressure frozen and freeze substituted
High pressure freezingInstrument: OTHER
Details: The value given for _emd_high_pressure_freezing.instrument is HPM100. This is not in a list of allowed values {'EMS-002 RAPID IMMERSION FREEZER', 'OTHER', 'LEICA EM PACT', 'LEICA EM HPM100', ...Details: The value given for _emd_high_pressure_freezing.instrument is HPM100. This is not in a list of allowed values {'EMS-002 RAPID IMMERSION FREEZER', 'OTHER', 'LEICA EM PACT', 'LEICA EM HPM100', 'LEICA EM PACT2', 'BAL-TEC HPM 010'} so OTHER is written into the XML file.
Cryo protectantBSA
SectioningUltramicrotomy - Instrument: Leica EM UC7 / Ultramicrotomy - Temperature: 20 K / Ultramicrotomy - Final thickness: 300 nm
Fiducial markerManufacturer: EMS / Diameter: 10 nm

-
Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 19.38 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 37

+
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