[English] 日本語
Yorodumi
- EMDB-11948: Axonemal 96nm-repeat from active flagella of wild type mouse, sho... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11948
TitleAxonemal 96nm-repeat from active flagella of wild type mouse, showing inner dynein arms (IDAs) in pre-power stroke conformations. Reconstruction obtained with classification and averaging of sub-tomograms from cryo-electron tomograms of wild type active flagella.
Map dataAxonemal 96nm-repeat from active flagella of wild type mouse, showing inner dynein arms (IDAs) in pre-power stroke conformations.
Sample
  • Complex: Axonemal 96nm-repeat
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 30.7 Å
AuthorsGadadhar S / Alvarez Viar G / Hansen JN / Gong A / Kostarev A / Ialy-Radio C / Leboucher S / Whitfield M / Ziyyat A / Toure A ...Gadadhar S / Alvarez Viar G / Hansen JN / Gong A / Kostarev A / Ialy-Radio C / Leboucher S / Whitfield M / Ziyyat A / Toure A / Alvarez L / Pigino G / Janke C
Funding support1 items
OrganizationGrant numberCountry
European Research Council (ERC)819826
CitationJournal: Science / Year: 2021
Title: Tubulin glycylation controls axonemal dynein activity, flagellar beat, and male fertility.
Authors: Sudarshan Gadadhar / Gonzalo Alvarez Viar / Jan Niklas Hansen / An Gong / Aleksandr Kostarev / Côme Ialy-Radio / Sophie Leboucher / Marjorie Whitfield / Ahmed Ziyyat / Aminata Touré / Luis ...Authors: Sudarshan Gadadhar / Gonzalo Alvarez Viar / Jan Niklas Hansen / An Gong / Aleksandr Kostarev / Côme Ialy-Radio / Sophie Leboucher / Marjorie Whitfield / Ahmed Ziyyat / Aminata Touré / Luis Alvarez / Gaia Pigino / Carsten Janke /
Abstract: Posttranslational modifications of the microtubule cytoskeleton have emerged as key regulators of cellular functions, and their perturbations have been linked to a growing number of human pathologies. ...Posttranslational modifications of the microtubule cytoskeleton have emerged as key regulators of cellular functions, and their perturbations have been linked to a growing number of human pathologies. Tubulin glycylation modifies microtubules specifically in cilia and flagella, but its functional and mechanistic roles remain unclear. In this study, we generated a mouse model entirely lacking tubulin glycylation. Male mice were subfertile owing to aberrant beat patterns of their sperm flagella, which impeded the straight swimming of sperm cells. Using cryo-electron tomography, we showed that lack of glycylation caused abnormal conformations of the dynein arms within sperm axonemes, providing the structural basis for the observed dysfunction. Our findings reveal the importance of microtubule glycylation for controlled flagellar beating, directional sperm swimming, and male fertility.
History
DepositionNov 17, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateJan 20, 2021-
Current statusJan 20, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 6.12
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11948.png

Downloads & links

-
Map

FileDownload / File: emd_11948.map.gz / Format: CCP4 / Size: 3.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAxonemal 96nm-repeat from active flagella of wild type mouse, showing inner dynein arms (IDAs) in pre-power stroke conformations.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
9.42 Å/pix.
x 88 pix.
= 829.136 Å		9.42 Å/pix.
x 160 pix.
= 1507.52 Å		9.42 Å/pix.
x 72 pix.
= 678.384 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 9.422 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.12 / Movie #1: 6.12
Minimum - Maximum-40.844482 - 43.06595
Average (Standard dev.)1.0526515 (±7.9630036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin04346
Dimensions1607288
Spacing7216088
CellA: 678.384 Å / B: 1507.52 Å / C: 829.136 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z9.4229.4229.422
M x/y/z7216088
origin x/y/z0.0000.0000.000
length x/y/z678.3841507.520829.136
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS43046
NC/NR/NS7216088
D min/max/mean-40.84443.0661.053

-
Supplemental data

-
Sample components

-
Entire : Axonemal 96nm-repeat

EntireName: Axonemal 96nm-repeat
Components
  • Complex: Axonemal 96nm-repeat

-
Supramolecule #1: Axonemal 96nm-repeat

SupramoleculeName: Axonemal 96nm-repeat / type: complex / ID: 1 / Parent: 0
Details: Axonemal 96nm-repeat from active flagella of wild type mouse, showing inner dynein arms (IDAs) in pre-power stroke conformations. Reconstruction obtained with classification and averaging of ...Details: Axonemal 96nm-repeat from active flagella of wild type mouse, showing inner dynein arms (IDAs) in pre-power stroke conformations. Reconstruction obtained with classification and averaging of sub-tomograms from cryo-electron tomograms of wild type active flagella.
Source (natural)Organism: Mus musculus (house mouse) / Strain: wild type / Tissue: Sperm cell / Organelle: flagellum

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 7.4 / Component - Name: PBS
GridModel: Quantifoil R3.5/1 / Material: GOLD / Support film - Material: CARBON
VitrificationCryogen name: ETHANE-PROPANE
DetailsFlagellated sperm cells from mouse

-
Electron microscopy

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 100.0 e/Å2

-
Image processing

ExtractionNumber tomograms: 7 / Number images used: 529
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 30.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 529

+
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