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- EMDB-35210: In situ structure of A-tubule of axonemal doublet microtubules in... -

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Basic information

Entry
Database: EMDB / ID: EMD-35210
TitleIn situ structure of A-tubule of axonemal doublet microtubules in mouse sperm with 16-nm repeat
Map dataA-tubule of axonemal doublet microtubules in mouse sperm with 16-nm repeat
Sample
  • Cell: mouse sperm
Keywordsmicrotubules / axoneme / sperm / filament / PROTEIN TRANSPORT
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 4.5 Å
AuthorsZhu Y / Tai LH / Yin GL / Sun F
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31925026 China
CitationJournal: Cell Discov / Year: 2023
Title: In-cell structural insight into the stability of sperm microtubule doublet.
Authors: Linhua Tai / Guoliang Yin / Xiaojun Huang / Fei Sun / Yun Zhu /
Abstract: The propulsion for mammalian sperm swimming is generated by flagella beating. Microtubule doublets (DMTs) along with microtubule inner proteins (MIPs) are essential structural blocks of flagella. ...The propulsion for mammalian sperm swimming is generated by flagella beating. Microtubule doublets (DMTs) along with microtubule inner proteins (MIPs) are essential structural blocks of flagella. However, the intricate molecular architecture of intact sperm DMT remains elusive. Here, by in situ cryo-electron tomography, we solved the in-cell structure of mouse sperm DMT at 4.5-7.5 Å resolutions, and built its model with 36 kinds of MIPs in 48 nm periodicity. We identified multiple copies of Tektin5 that reinforce Tektin bundle, and multiple MIPs with different periodicities that anchor the Tektin bundle to tubulin wall. This architecture contributes to a superior stability of A-tubule than B-tubule of DMT, which was revealed by structural comparison of DMTs from the intact and deformed axonemes. Our work provides an overall molecular picture of intact sperm DMT in 48 nm periodicity that is essential to understand the molecular mechanism of sperm motility as well as the related ciliopathies.
History
DepositionJan 31, 2023-
Header (metadata) releaseOct 11, 2023-
Map releaseOct 11, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35210.png

Downloads & links

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Map

FileDownload / File: emd_35210.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA-tubule of axonemal doublet microtubules in mouse sperm with 16-nm repeat
Voxel sizeX=Y=Z: 1.76 Å
Density
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.006632351 - 0.014235034
Average (Standard dev.)0.0009765103 (±0.0018446062)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 380.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_35210_msk_1.map
Projections & Slices
AxesZYX

Projections

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Histogram

Histogram (log scale)

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Half map: Half 1 map of mouse sperm DMT A-tubule

Fileemd_35210_half_map_1.map
AnnotationHalf 1 map of mouse sperm DMT A-tubule
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half 2 map of mouse sperm DMT A-tubule

Fileemd_35210_half_map_2.map
AnnotationHalf 2 map of mouse sperm DMT A-tubule
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mouse sperm

EntireName: mouse sperm
Components
  • Cell: mouse sperm

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Supramolecule #1: mouse sperm

SupramoleculeName: mouse sperm / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 3.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 689 / Number images used: 37018
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 37018
FSC plot (resolution estimation)

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