[English] 日本語
Yorodumi
- EMDB-5482: Cryo electron tomography of sensory cilia in normal and diseased ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5482
TitleCryo electron tomography of sensory cilia in normal and diseased retinas
Map dataReconstruction of rootletin knockout mouse photoreceptor primary cilium
Sample
  • Sample: Rootletin knockout mouse photoreceptor primary cilium
  • Organelle or cellular component: Photoreceptor primary cilium
Keywordsphotoreceptor primary cilium / cryo electron tomography / rod outer segment / mouse / cilia / axoneme / retina / photoreceptor
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsGilliam JC / Chang JT / Sandoval IM / Zhang Y / Li T / Pittler SJ / Chiu W / Wensel TG
CitationJournal: Cell / Year: 2012
Title: Three-dimensional architecture of the rod sensory cilium and its disruption in retinal neurodegeneration.
Authors: Jared C Gilliam / Juan T Chang / Ivette M Sandoval / Youwen Zhang / Tiansen Li / Steven J Pittler / Wah Chiu / Theodore G Wensel /
Abstract: Defects in primary cilia lead to devastating disease because of their roles in sensation and developmental signaling but much is unknown about ciliary structure and mechanisms of their formation and ...Defects in primary cilia lead to devastating disease because of their roles in sensation and developmental signaling but much is unknown about ciliary structure and mechanisms of their formation and maintenance. We used cryo-electron tomography to obtain 3D maps of the connecting cilium and adjacent cellular structures of a modified primary cilium, the rod outer segment, from wild-type and genetically defective mice. The results reveal the molecular architecture of the cilium and provide insights into protein functions. They suggest that the ciliary rootlet is involved in cellular transport and stabilizes the axoneme. A defect in the BBSome membrane coat caused defects in vesicle targeting near the base of the cilium. Loss of the proteins encoded by the Cngb1 gene disrupted links between the disk and plasma membranes. The structures of the outer segment membranes support a model for disk morphogenesis in which basal disks are enveloped by the plasma membrane.
History
DepositionAug 23, 2012-
Header (metadata) releaseSep 5, 2012-
Map releaseDec 12, 2012-
UpdateDec 12, 2012-
Current statusDec 12, 2012Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_5482.map.gz / Format: CCP4 / Size: 289.1 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationReconstruction of rootletin knockout mouse photoreceptor primary cilium
Voxel sizeX=Y=Z: 28.63 Å
Density
Minimum - Maximum-4182.0 - 3136.0
Average (Standard dev.)216.655899049999988 (±119.635070799999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin7400
Dimensions14810241024
Spacing14810241024
CellA: 29317.12 Å / B: 4237.2397 Å / C: 29317.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z28.62999902343728.6328.629999023437
M x/y/z10241481024
origin x/y/z0.0000.0000.000
length x/y/z29317.1194237.24029317.119
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S123
start NC/NR/NS0740
NC/NR/NS10241481024
D min/max/mean-4182.0003136.000216.656

-
Supplemental data

-
Sample components

-
Entire : Rootletin knockout mouse photoreceptor primary cilium

EntireName: Rootletin knockout mouse photoreceptor primary cilium
Components
  • Sample: Rootletin knockout mouse photoreceptor primary cilium
  • Organelle or cellular component: Photoreceptor primary cilium

-
Supramolecule #1000: Rootletin knockout mouse photoreceptor primary cilium

SupramoleculeName: Rootletin knockout mouse photoreceptor primary cilium / type: sample / ID: 1000 / Number unique components: 1

-
Supramolecule #1: Photoreceptor primary cilium

SupramoleculeName: Photoreceptor primary cilium / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Mus musculus (house mouse) / Strain: mixed C57BL/6 x 129/Sv background / synonym: mouse / Tissue: retina

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography

-
Sample preparation

GridDetails: 200 mesh copper grid with holey carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeJEOL 2100
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal magnification: 15000
Sample stageSpecimen holder: Liquid nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -64 ° / Tilt series - Axis1 - Max angle: 64 ° / Tilt series - Axis1 - Angle increment: 2 °
DateFeb 14, 2009
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN / Number real images: 65 / Average electron dose: 53 e/Å2

-
Image processing

Final reconstructionAlgorithm: OTHER / Software - Name: IMOD / Number images used: 65
DetailsStandard IMOD fiducial alignment with weighted back projection

+
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