[English] 日本語
Yorodumi
- EMDB-13061: Tomogram of nuclear envelope of MEF cell carrying homozygous H222... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13061
TitleTomogram of nuclear envelope of MEF cell carrying homozygous H222P mutation in Lmna.
Map dataTomogram of nuclear envelope of MEF carrying LmnaH222P/H222P mutation.
Sample
  • Cell: H222P MEF
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsKronenberg-Tenga R
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationSNSF 31003A_179418 Switzerland
CitationJournal: J Cell Sci / Year: 2021
Title: A lamin A/C variant causing striated muscle disease provides insights into filament organization.
Authors: Rafael Kronenberg-Tenga / Meltem Tatli / Matthias Eibauer / Wei Wu / Ji-Yeon Shin / Gisèle Bonne / Howard J Worman / Ohad Medalia /
Abstract: The gene encodes the A-type lamins, which polymerize into ∼3.5-nm-thick filaments and, together with B-type lamins and associated proteins, form the nuclear lamina. Mutations in cause a wide ...The gene encodes the A-type lamins, which polymerize into ∼3.5-nm-thick filaments and, together with B-type lamins and associated proteins, form the nuclear lamina. Mutations in cause a wide variety of pathologies. In this study, we analyzed the nuclear lamina of embryonic fibroblasts from mice, which develop cardiomyopathy and muscular dystrophy. Although the organization of the lamina appeared unaltered, there were changes in chromatin and B-type lamin expression. An increase in nuclear size and consequently a relative reduction in heterochromatin near the lamina allowed for a higher resolution structural analysis of lamin filaments using cryo-electron tomography. This was most apparent when visualizing lamin filaments and using a nuclear extraction protocol. Averaging of individual segments of filaments in mouse fibroblasts resolved two polymers that constitute the mature filaments. Our findings provide better views of the organization of lamin filaments and the effect of a striated muscle disease-causing mutation on nuclear structure.
History
DepositionJun 10, 2021-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateJun 22, 2022-
Current statusJun 22, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_13061.png

Downloads & links

-
Map

FileDownload / File: emd_13061.map.gz / Format: CCP4 / Size: 662.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram of nuclear envelope of MEF carrying LmnaH222P/H222P mutation.
Voxel sizeX=Y=Z: 8.82603 Å
Density
Minimum - Maximum-3366.405 - 2024.2427
Average (Standard dev.)38.223618 (±65.75597)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin9716-16
Dimensions195960928
Spacing960195928
CellA: 8472.988 Å / B: 1721.0758 Å / C: 8190.5557 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : H222P MEF

EntireName: H222P MEF
Components
  • Cell: H222P MEF

-
Supramolecule #1: H222P MEF

SupramoleculeName: H222P MEF / type: cell / ID: 1 / Parent: 0
Details: MEF cell carrying homozygous H222P mutation in Lmna.
Source (natural)Organism: Mus musculus (house mouse)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: GOLD
VitrificationCryogen name: ETHANE
DetailsMEF cell carrying homozygous H222P mutation in Lmna.
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.24 nA / Focused ion beam - Duration: 3600 sec. / Focused ion beam - Temperature: 128 K / Focused ion beam - Initial thickness: 4000 nm / Focused ion beam - Final thickness: 200 nm
Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is Zeiss Auriga. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 3.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: IMOD / Number images used: 41

+
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://pdbjlvh1.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