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- EMDB-11945: Post-post-power stroke conformation of the mouse sperm outer dyne... -

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Basic information

Entry
Database: EMDB / ID: EMD-11945
TitlePost-post-power stroke conformation of the mouse sperm outer dynein arms (ODAs), with both gamma-heavy chain and beta-heavy chain in post-power stroke conformation. Reconstruction obtained with sub-tomogram classification and averaging from cryo-electron tomograms of active flagella of mouse sperm cells.
Map dataPost-post-power stroke conformation of the mouse sperm outer dynein arms (ODAs), with both gamma- and beta-heavy chains in post-power stroke conformation.
Sample
  • Complex: axonemal outer dynein arm (ODA)
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 34.5 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 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: 4.28
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.28
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11945.png

Downloads & links

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Map

FileDownload / File: emd_11945.map.gz / Format: CCP4 / Size: 695.3 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-post-power stroke conformation of the mouse sperm outer dynein arms (ODAs), with both gamma- and beta-heavy chains in post-power stroke conformation.
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.28 / Movie #1: 4.28
Minimum - Maximum-11.713591 - 15.533178
Average (Standard dev.)1.6213804 (±4.25252)
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-11.71415.5331.621

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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)
Components
  • Complex: axonemal outer dynein arm (ODA)

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Supramolecule #1: axonemal outer dynein arm (ODA)

SupramoleculeName: axonemal outer dynein arm (ODA) / type: complex / ID: 1 / Parent: 0
Details: Post-post-power stroke conformation of the mouse sperm outer dynein arms (ODAs), with both gamma-heavy chain and beta-heavy chain in post-power stroke conformation. Reconstruction obtained ...Details: Post-post-power stroke conformation of the mouse sperm outer dynein arms (ODAs), with both gamma-heavy chain and beta-heavy chain in post-power stroke conformation. Reconstruction obtained with sub-tomogram classification and averaging from cryo-electron tomograms of active flagella of mouse sperm cells.
Source (natural)Organism: Mus musculus (house mouse) / Strain: Wild type / Tissue: Sperm cell / Organelle: flagellum

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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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

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Electron microscopy

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

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 34.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1016
ExtractionNumber tomograms: 7 / Number images used: 1016
Final angle assignmentType: NOT APPLICABLE

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