[English] 日本語
Yorodumi
- EMDB-5950: Cryo-electron tomography reveals ciliary defects underlying human... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5950
TitleCryo-electron tomography reveals ciliary defects underlying human RSPH1 primary ciliary dyskinesia
Map dataReconstruction of 96 nm axonemal repeat of normal human respiratory cilia
Sample
  • Sample: Normal human respiratory ciliary axonemes
  • Organelle or cellular component: Axoneme
Keywordsaxoneme / ciliopathy / human respiratory cilia / radial spoke / dynein
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 34.0 Å
AuthorsLin J / Yin W / Smith MC / Song KK / Leigh MW / Zariwala MA / Knowles MR / Ostrowski LE / Nicastro D
CitationJournal: Nat Commun / Year: 2014
Title: Cryo-electron tomography reveals ciliary defects underlying human RSPH1 primary ciliary dyskinesia.
Authors: Jianfeng Lin / Weining Yin / Maria C Smith / Kangkang Song / Margaret W Leigh / Maimoona A Zariwala / Michael R Knowles / Lawrence E Ostrowski / Daniela Nicastro /
Abstract: Cilia play essential roles in normal human development and health; cilia dysfunction results in diseases such as primary ciliary dyskinesia (PCD). Despite their importance, the native structure of ...Cilia play essential roles in normal human development and health; cilia dysfunction results in diseases such as primary ciliary dyskinesia (PCD). Despite their importance, the native structure of human cilia is unknown, and structural defects in the cilia of patients are often undetectable or remain elusive because of heterogeneity. Here we develop an approach that enables visualization of human (patient) cilia at high-resolution using cryo-electron tomography of samples obtained noninvasively by nasal scrape biopsy. We present the native 3D structures of normal and PCD-causing RSPH1-mutant human respiratory cilia in unprecedented detail; this allows comparisons of cilia structure across evolutionarily distant species and reveals the previously unknown primary defect and the heterogeneous secondary defects in RSPH1-mutant cilia. Our data provide evidence for structural and functional heterogeneity in radial spokes, suggest a mechanism for the milder RSPH1 PCD phenotype and demonstrate that cryo-electron tomography can be applied to human disease by directly imaging patient samples.
History
DepositionApr 18, 2014-
Header (metadata) releaseJul 30, 2014-
Map releaseDec 10, 2014-
UpdateDec 17, 2014-
Current statusDec 17, 2014Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 139
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 139
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5950.tif

Downloads & links

-
Map

FileDownload / File: emd_5950.map.gz / Format: CCP4 / Size: 3.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of 96 nm axonemal repeat of normal human respiratory cilia
Voxel sizeX=Y=Z: 9.997 Å
Density
Contour LevelBy AUTHOR: 139.0 / Movie #1: 139
Minimum - Maximum100.554534910000001 - 181.249450679999995
Average (Standard dev.)134.672790529999986 (±6.80494785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-25-1-35
Dimensions8614086
Spacing8614086
CellA: 1399.58 Å / B: 859.742 Å / C: 859.742 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z9.9979.9979.997
M x/y/z1408686
origin x/y/z0.0000.0000.000
length x/y/z1399.580859.742859.742
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS-1-25-35
NC/NR/NS1408686
D min/max/mean100.555181.249134.673

-
Supplemental data

-
Sample components

-
Entire : Normal human respiratory ciliary axonemes

EntireName: Normal human respiratory ciliary axonemes
Components
  • Sample: Normal human respiratory ciliary axonemes
  • Organelle or cellular component: Axoneme

-
Supramolecule #1000: Normal human respiratory ciliary axonemes

SupramoleculeName: Normal human respiratory ciliary axonemes / type: sample / ID: 1000
Details: The samples were normal human respiratory ciliary axonemes isolated from cultures of trachea-bronchial epithelial cells.
Number unique components: 1

-
Supramolecule #1: Axoneme

SupramoleculeName: Axoneme / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Trachea-bronchial / Cell: Epithelial cells / Organelle: Cilia

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 7.3
Details: 30 mM Hepes, pH 7.3, 1 mM EGTA, 5 mM MgSO4, 0.1 mM EDTA, 25 mM NaCl, 1 mM dithiothreitol, 1% protease inhibitor cocktail, 100 g/mL soybean trypsin inhibitor (Sigma T9128)
GridDetails: Quantifoil holey carbon grids Cu 200 mesh R2/2
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER / Method: Blot for 1.5-2.5 seconds before plunging

-
Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 8.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 13500
Specialist opticsEnergy filter - Name: GATAN postcolumn filter GIF / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -65 ° / Tilt series - Axis1 - Max angle: 65 °
DateFeb 5, 2013
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Average electron dose: 100 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 34.0 Å / Resolution method: OTHER / Software - Name: IMOD
Details: Final map was calculated by averaging 850 particles (96-nm-long axonemal repeats) from 12 tomograms.
Number subtomograms used: 950
Details3D tomograms were reconstructed using fiducial alignment and weighted backprojection using IMOD software. Final maps were calculated by averaging 950 particles (96-nm-long axonemal repeats) from 12 tomograms using the PEET software.

+
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