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- EMDB-11946: Axonemal 96nm-repeat from active sperm flagella of wild type mous... -

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Basic information

Entry
Database: EMDB / ID: EMD-11946
TitleAxonemal 96nm-repeat from active sperm flagella of wild type mouse. Reconstruction obtained with cryo-ET and sub-tomogram averaging.
Map data
SampleAxonemal 96nm-repeat
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 24 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: 4.66
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.66
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11946.png

Downloads & links

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Map

FileDownload / File: emd_11946.map.gz / Format: CCP4 / Size: 4 MB / 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 88 pix.
= 829.136 Å		9.42 Å/pix.
x 160 pix.
= 1507.52 Å		9.42 Å/pix.
x 74 pix.
= 697.228 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: 4.66 / Movie #1: 4.66
Minimum - Maximum-42.31181 - 45.27
Average (Standard dev.)0.7254494 (±8.373621)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin04346
Dimensions1607488
Spacing7416088
CellA: 697.22797 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/z7416088
origin x/y/z0.0000.0000.000
length x/y/z697.2281507.520829.136
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS43046
NC/NR/NS7416088
D min/max/mean-42.31245.2700.725

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Supplemental data

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Sample components

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Entire Axonemal 96nm-repeat

EntireName: Axonemal 96nm-repeat
Details: Axonemal 96nm-repeat from active sperm flagella of wild type mouse. Reconstruction obtained with cryo-ET and sub-tomogram averaging.
Number of components: 1

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Component #1: protein, Axonemal 96nm-repeat

ProteinName: Axonemal 96nm-repeat
Details: Axonemal 96nm-repeat from active sperm flagella of wild type mouse. Reconstruction obtained with cryo-ET 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 / Number of subtomograms: 900
3D reconstructionResolution: 24 Å / Resolution method: FSC 0.143 CUT-OFF

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