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- EMDB-27462: 96-nm repeating structure of microtubule doublet from human sperm -

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Basic information

Entry
Database: EMDB / ID: EMD-27462
Title96-nm repeating structure of microtubule doublet from human sperm
Map data
Sample
  • Complex: Microtubule doublet from mouse sperm
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 23.0 Å
AuthorsChen Z / Greenan AG / Shiozak M / Liu Y / Skinner W / Zhao X / Zhao S / Yan R / Guo C / Yu Z ...Chen Z / Greenan AG / Shiozak M / Liu Y / Skinner W / Zhao X / Zhao S / Yan R / Guo C / Yu Z / Lishko PV / Agard DA / Vale RD
Funding support United States, 4 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118106 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118099 United States
The Pew Charitable TrustsPew Biomedical Scholar Award United States
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: In situ cryo-electron tomography reveals the asymmetric architecture of mammalian sperm axonemes.
Authors: Zhen Chen / Garrett A Greenan / Momoko Shiozaki / Yanxin Liu / Will M Skinner / Xiaowei Zhao / Shumei Zhao / Rui Yan / Zhiheng Yu / Polina V Lishko / David A Agard / Ronald D Vale /
Abstract: The flagella of mammalian sperm display non-planar, asymmetric beating, in contrast to the planar, symmetric beating of flagella from sea urchin sperm and unicellular organisms. The molecular basis ...The flagella of mammalian sperm display non-planar, asymmetric beating, in contrast to the planar, symmetric beating of flagella from sea urchin sperm and unicellular organisms. The molecular basis of this difference is unclear. Here, we perform in situ cryo-electron tomography of mouse and human sperm, providing the highest-resolution structural information to date. Our subtomogram averages reveal mammalian sperm-specific protein complexes within the microtubules, the radial spokes and nexin-dynein regulatory complexes. The locations and structures of these complexes suggest potential roles in enhancing the mechanical strength of mammalian sperm axonemes and regulating dynein-based axonemal bending. Intriguingly, we find that each of the nine outer microtubule doublets is decorated with a distinct combination of sperm-specific complexes. We propose that this asymmetric distribution of proteins differentially regulates the sliding of each microtubule doublet and may underlie the asymmetric beating of mammalian sperm.
History
DepositionJul 1, 2022-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateMar 29, 2023-
Current statusMar 29, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27462.png

Downloads & links

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Map

FileDownload / File: emd_27462.map.gz / Format: CCP4 / Size: 22.2 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.)
7.98 Å/pix.
x 180 pix.
= 1436.4 Å		7.98 Å/pix.
x 180 pix.
= 1436.4 Å		7.98 Å/pix.
x 180 pix.
= 1436.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 7.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.067
Minimum - Maximum-0.45665476 - 0.52265203
Average (Standard dev.)0.00046110988 (±0.04128881)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 1436.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_27462_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_27462_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Microtubule doublet from mouse sperm

EntireName: Microtubule doublet from mouse sperm
Components
  • Complex: Microtubule doublet from mouse sperm

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Supramolecule #1: Microtubule doublet from mouse sperm

SupramoleculeName: Microtubule doublet from mouse sperm / type: complex / ID: 1 / Chimera: Yes / Parent: 0
Source (natural)Organism: Mus musculus (house mouse) / Strain: C57Bl/6J
Molecular weightTheoretical: 30 MDa

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 7.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0) / Number subtomograms used: 6613
ExtractionNumber tomograms: 86 / Number images used: 39844
Final angle assignmentType: MAXIMUM LIKELIHOOD

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