[English] 日本語
Yorodumi
- EMDB-12958: Cryo-tomogram showing the modulation of the K5/K14 keratin networ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12958
TitleCryo-tomogram showing the modulation of the K5/K14 keratin network in a keratinocyte ghost cell
Map dataCryo-tomogram showing the modulation of the K5/K14 keratin network in a keratinocyte ghost cell
Sample
  • Cell: Keratin network in a detergent permeabilized K5/K14_1 cell
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsWeber MS / Eibauer M / Medalia O
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A, 179418 Switzerland
University of ZurichFK-18-041 Switzerland
CitationJournal: Elife / Year: 2021
Title: Structural heterogeneity of cellular K5/K14 filaments as revealed by cryo-electron microscopy.
Authors: Miriam S Weber / Matthias Eibauer / Suganya Sivagurunathan / Thomas M Magin / Robert D Goldman / Ohad Medalia /
Abstract: Keratin intermediate filaments are an essential and major component of the cytoskeleton in epithelial cells. They form a stable yet dynamic filamentous network extending from the nucleus to the cell ...Keratin intermediate filaments are an essential and major component of the cytoskeleton in epithelial cells. They form a stable yet dynamic filamentous network extending from the nucleus to the cell periphery, which provides resistance to mechanical stresses. Mutations in keratin genes are related to a variety of epithelial tissue diseases. Despite their importance, the molecular structure of keratin filaments remains largely unknown. In this study, we analyzed the structure of keratin 5/keratin 14 filaments within ghost mouse keratinocytes by cryo-electron microscopy and cryo-electron tomography. By averaging a large number of keratin segments, we have gained insights into the helical architecture of the filaments. Two-dimensional classification revealed profound variations in the diameter of keratin filaments and their subunit organization. Computational reconstitution of filaments of substantial length uncovered a high degree of internal heterogeneity along single filaments, which can contain regions of helical symmetry, regions with less symmetry and regions with significant diameter fluctuations. Cross-section views of filaments revealed that keratins form hollow cylinders consisting of multiple protofilaments, with an electron dense core located in the center of the filament. These findings shed light on the complex and remarkable heterogenic architecture of keratin filaments, suggesting that they are highly flexible, dynamic cytoskeletal structures.
History
DepositionMay 17, 2021-
Header (metadata) releaseAug 18, 2021-
Map releaseAug 18, 2021-
UpdateAug 25, 2021-
Current statusAug 25, 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_12958.png

Downloads & links

-
Map

FileDownload / File: emd_12958.map.gz / Format: CCP4 / Size: 531 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationCryo-tomogram showing the modulation of the K5/K14 keratin network in a keratinocyte ghost cell
Voxel sizeX=Y=Z: 7.00289 Å
Density
Minimum - Maximum-126.0 - 125.0
Average (Standard dev.)-66.13832 (±8.831876)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions928960625
Spacing960928625
CellA: 6722.7744 Å / B: 6498.682 Å / C: 4376.806 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z7.00288958333337.00289008620697.0028896
M x/y/z960928625
origin x/y/z0.0000.0000.000
length x/y/z6722.7746498.6824376.806
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ250250250
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS960928625
D min/max/mean-126.000125.000-66.138

-
Supplemental data

-
Sample components

-
Entire : Keratin network in a detergent permeabilized K5/K14_1 cell

EntireName: Keratin network in a detergent permeabilized K5/K14_1 cell
Components
  • Cell: Keratin network in a detergent permeabilized K5/K14_1 cell

-
Supramolecule #1: Keratin network in a detergent permeabilized K5/K14_1 cell

SupramoleculeName: Keratin network in a detergent permeabilized K5/K14_1 cell
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse) / Organ: Skin / Tissue: Epidermis

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
GridDetails: Cells were grown on grids overnight at 32 degree and 5% CO2 and permeabilized and plunge frozen on the next day.
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion, Netherlands / Diameter: 10 nm

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 0.8 sec. / Average electron dose: 2.17 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 28571
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.10.51) / Number images used: 41
CTF correctionSoftware - Name: IMOD (ver. 4.10.51)

+
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