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- EMDB-11943: ""Tubulin glycylation controls axonemal dynein activity, flagella... -

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Basic information

Entry
Database: EMDB / ID: EMD-11943
Title"Tubulin glycylation controls axonemal dynein activity, flagellar beat and male fertility": Pre-post-power stroke conformation of the mouse sperm outer dynein arms (ODAs), with gamma-heavy chain in pre-power stroke conformation and beta-heavy chain in post-power stroke conformation. Cryo-ET, classification and sub-tomogram averaging.
Map data
Sampleaxonemal outer dynein arm (ODA)
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 35.7 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.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionNov 16, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateJan 20, 2021-
Current statusJan 20, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_11943.map.gz / Format: CCP4 / Size: 695.3 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
9.42 Å/pix.
x 39 pix.
= 367.458 Å
9.42 Å/pix.
x 60 pix.
= 565.32 Å
9.42 Å/pix.
x 76 pix.
= 716.072 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
Contour LevelBy AUTHOR: 3.03 / Movie #1: 3.03
Minimum - Maximum-16.512577 - 21.150082
Average (Standard dev.)1.5756351 (±5.275267)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin03210
Dimensions607639
Spacing766039
CellA: 716.072 Å / B: 565.32 Å / C: 367.458 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z9.4229.4229.422
M x/y/z766039
origin x/y/z0.0000.0000.000
length x/y/z716.072565.320367.458
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS32010
NC/NR/NS766039
D min/max/mean-16.51321.1501.576

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Supplemental data

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Sample components

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Entire axonemal outer dynein arm (ODA)

EntireName: axonemal outer dynein arm (ODA)
Details: Pre-post-power stroke conformation of the mouse sperm outer dynein arms (ODAs), with gamma-heavy chain in pre-power stroke conformation and beta-heavy chain in post-power stroke conformation. ...Details: Pre-post-power stroke conformation of the mouse sperm outer dynein arms (ODAs), with gamma-heavy chain in pre-power stroke conformation and beta-heavy chain in post-power stroke conformation. Reconstructed with cryo-ET, classification and sub-tomogram averaging.
Number of components: 1

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Component #1: protein, axonemal outer dynein arm (ODA)

ProteinName: axonemal outer dynein arm (ODA)
Details: Pre-post-power stroke conformation of the mouse sperm outer dynein arms (ODAs), with gamma-heavy chain in pre-power stroke conformation and beta-heavy chain in post-power stroke conformation. ...Details: Pre-post-power stroke conformation of the mouse sperm outer dynein arms (ODAs), with gamma-heavy chain in pre-power stroke conformation and beta-heavy chain in post-power stroke conformation. Reconstructed with cryo-ET, classification and sub-tomogram averaging.
Recombinant expression: No
SourceSpecies: Mus musculus (house mouse) / Strain: Wild type
Source (natural)Organelle: flagellum / Organ or tissue: Sperm cell

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Experimental details

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Sample preparation

SpecimenSpecimen state: Cell / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: OTHER

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 100 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 7
3D reconstructionResolution: 35.7 Å / Resolution method: FSC 0.143 CUT-OFF

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