[English] 日本語
Yorodumi
- EMDB-18122: A cryo-ET study of ciliary rootlet organization - purified rootle... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18122
TitleA cryo-ET study of ciliary rootlet organization - purified rootlet example 1
Map datapurified rootlet, eman2 preprocessed cropped tomogram for segmentation. Object files are found on biostudies (S-BSST1164, https://www.ebi.ac.uk/biostudies/studies/S-BSST1164)
Sample
  • Organelle or cellular component: Ciliary rootlet surrounded by cellular membranes
Keywordsciliary rootlet / rootlet / rootletin / centriole / cilia / STRUCTURAL PROTEIN
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
Authorsvan Hoorn C / Carter AP
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_A025_1011 United Kingdom
Wellcome Trust210711/Z/18/Z United Kingdom
CitationJournal: To Be Published
Title: A cryo-ET study of ciliary rootlet organization
Authors: van Hoorn C / Carter AP
History
DepositionAug 3, 2023-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateOct 18, 2023-
Current statusOct 18, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18122.png

Downloads & links

-
Map

FileDownload / File: emd_18122.map.gz / Format: CCP4 / Size: 59.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpurified rootlet, eman2 preprocessed cropped tomogram for segmentation. Object files are found on biostudies (S-BSST1164, https://www.ebi.ac.uk/biostudies/studies/S-BSST1164)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
11.1 Å/pix.
x 84 pix.
= 932.736 Å		11.1 Å/pix.
x 384 pix.
= 4263.936 Å		11.1 Å/pix.
x 480 pix.
= 5329.92 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 11.104 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-3.0 - 3.0
Average (Standard dev.)0.012492508 (±0.929045)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin172218127
Dimensions38448084
Spacing48038484
CellA: 5329.92 Å / B: 4263.936 Å / C: 932.736 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Ciliary rootlet surrounded by cellular membranes

EntireName: Ciliary rootlet surrounded by cellular membranes
Components
  • Organelle or cellular component: Ciliary rootlet surrounded by cellular membranes

-
Supramolecule #1: Ciliary rootlet surrounded by cellular membranes

SupramoleculeName: Ciliary rootlet surrounded by cellular membranes / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Details: The sample was purified according to https://doi.org/10.1016/j.cell.2012.10.038, maintaining cellular interactions with the rootlet.
Source (natural)Organism: Mus musculus (house mouse) / Organ: eye / Tissue: retina / Organelle: rootlet / Location in cell: centriole associated, cytoplasm

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: BBI / Diameter: 10 nm

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.68 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

DetailsFor tomogram segmentation, tomograms were reconstructed as even/odd frame half tomograms using the above mentioned WARP pipeline and denoised using Noise2Map(Tegunov & Cramer, 2018). The tomograms were then deconvolved and isotropically reconstructed with denoising using IsoNet(Liu et al, 2021) with a cube size of 128 pixels. The tomograms were then preprocessed in EMAN2.2 for training of the TomoSeg CNN(Chen et al, 2017).
Final reconstructionNumber 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://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