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- EMDB-60455: Cmb part of the central apparatus in mouse sperm axoneme -

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Basic information

Entry
Database: EMDB / ID: EMD-60455
TitleCmb part of the central apparatus in mouse sperm axoneme
Map data
Sample
  • Cell: mouse sperm
Keywordsmicrotubules / axoneme / sperm / filament / PROTEIN TRANSPORT
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 15.0 Å
AuthorsZhu Y / Yin GL / Tai LH / Sun F
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31925026 China
CitationJournal: Cell Res / Year: 2025
Title: In situ structure of the mouse sperm central apparatus reveals mechanistic insights into asthenozoospermia.
Authors: Yun Zhu / Tingting Lin / Guoliang Yin / Linhua Tai / Lianwan Chen / Jing Ma / Guoning Huang / Yi Lu / Zhiyong Zhang / Binbin Wang / Suren Chen / Fei Sun /
Abstract: The central apparatus (CA) within the sperm axoneme is vital for sperm motility, yet its molecular architecture and functional mechanisms remain incompletely understood. Combining cryo-electron ...The central apparatus (CA) within the sperm axoneme is vital for sperm motility, yet its molecular architecture and functional mechanisms remain incompletely understood. Combining cryo-electron tomography and AlphaFold2, we resolved the in-cell structure of mouse sperm CA at a subnanometer resolution and built a near-complete atomic model. Our analysis identified 39 CA-associated proteins, including eight previously unreported components. By presenting the full-length structures of CFAP47 and HYDIN, we elucidate their molecular roles in tethering the C1 and C2 microtubules within the CA. Specifically, HYDIN forms a semicircular chain that encircles C1 and C2, with its N-terminal half driving the C1-C2 connection and its C-terminal half providing axial support in C2. CFAP47, the core structural component of the bridge, binds C1 through its N-terminal domains, interacts with HYDIN via its central CFAP47-ring, and anchors to C2 through its C-terminal region. The significantly reduced sperm motility and impaired CA structure observed in Cfap47-knockout mice confirmed the important role of CFAP47. Furthermore, genetic analysis of infertile Chinese men with asthenozoospermia identified previously unreported mutations in the CFAP47. The CA structural model elucidates the pathogenic mechanisms of these mutations, establishing a direct link between CFAP47 dysfunction and impaired sperm motility. Therefore, our study provides mechanistic insights into CA-related fertility disorders.
History
DepositionJun 6, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60455.png

Downloads & links

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Map

FileDownload / File: emd_60455.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
3.52 Å/pix.
x 150 pix.
= 528. Å		3.52 Å/pix.
x 150 pix.
= 528. Å		3.52 Å/pix.
x 150 pix.
= 528. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.52 Å
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Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.0077825584 - 0.02251471
Average (Standard dev.)0.000061169194 (±0.0011412236)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 528.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60455_msk_1.map
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Half map: #1

Fileemd_60455_half_map_1.map
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Half map: #2

Fileemd_60455_half_map_2.map
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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
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 16000
ExtractionNumber tomograms: 1889 / Number images used: 105000
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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