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- EMDB-28606: 96nm doublet microtubule repeat from LRRC23-KO mouse sperm -

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Basic information

Entry
Database: EMDB / ID: EMD-28606
Title96nm doublet microtubule repeat from LRRC23-KO mouse sperm
Map datamasked map of 96nm doublet microtubule repeat from LRRC23-KO mouse sperm
Sample
  • Cell: Mouse sperm
Keywords96nm doublet microtubule repeat from LRRC23-KO mouse sperm / STRUCTURAL PROTEIN
Biological speciesMus (mice)
Methodsubtomogram averaging / cryo EM / Resolution: 27.0 Å
AuthorsHwang JY / Chai P / Nawaz S
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R01HD096745 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM142959 United States
CitationJournal: Elife / Year: 2023
Title: LRRC23 truncation impairs radial spoke 3 head assembly and sperm motility underlying male infertility.
Authors: Jae Yeon Hwang / Pengxin Chai / Shoaib Nawaz / Jungmin Choi / Francesc Lopez-Giraldez / Shabir Hussain / Kaya Bilguvar / Shrikant Mane / Richard P Lifton / Wasim Ahmad / Kai Zhang / Jean-Ju Chung /
Abstract: Radial spokes (RS) are T-shaped multiprotein complexes on the axonemal microtubules. Repeated RS1, RS2, and RS3 couple the central pair to modulate ciliary and flagellar motility. Despite the cell ...Radial spokes (RS) are T-shaped multiprotein complexes on the axonemal microtubules. Repeated RS1, RS2, and RS3 couple the central pair to modulate ciliary and flagellar motility. Despite the cell type specificity of RS3 substructures, their molecular components remain largely unknown. Here, we report that a leucine-rich repeat-containing protein, LRRC23, is an RS3 head component essential for its head assembly and flagellar motility in mammalian spermatozoa. From infertile male patients with defective sperm motility, we identified a splice site variant of . A mutant mouse model mimicking this variant produces a truncated LRRC23 at the C-terminus that fails to localize to the sperm tail, causing male infertility due to defective sperm motility. LRRC23 was previously proposed to be an ortholog of the RS stalk protein RSP15. However, we found that purified recombinant LRRC23 interacts with an RS head protein RSPH9, which is abolished by the C-terminal truncation. Evolutionary and structural comparison also shows that LRRC34, not LRRC23, is the RSP15 ortholog. Cryo-electron tomography clearly revealed that the absence of the RS3 head and the sperm-specific RS2-RS3 bridge structure in LRRC23 mutant spermatozoa. Our study provides new insights into the structure and function of RS3 in mammalian spermatozoa and the molecular pathogenicity of LRRC23 underlying reduced sperm motility in infertile human males.
History
DepositionOct 18, 2022-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateDec 27, 2023-
Current statusDec 27, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28606.png

Downloads & links

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Map

FileDownload / File: emd_28606.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmasked map of 96nm doublet microtubule repeat from LRRC23-KO mouse sperm
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.2 Å/pix.
x 160 pix.
= 1632. Å		10.2 Å/pix.
x 160 pix.
= 1632. Å		10.2 Å/pix.
x 160 pix.
= 1632. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 10.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.9253267 - 1.386112
Average (Standard dev.)0.013205768 (±0.10835184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 1632.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unmasked map of 96nm doublet microtubule repeat from...

Fileemd_28606_additional_1.map
Annotationunmasked map of 96nm doublet microtubule repeat from LRRC23-KO mouse sperm
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1 of 96nm doublet microtubule repeat...

Fileemd_28606_half_map_1.map
Annotationhalf map 1 of 96nm doublet microtubule repeat from LRRC23-KO mouse sperm
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2 of 96nm doublet microtubule repeat...

Fileemd_28606_half_map_2.map
Annotationhalf map 2 of 96nm doublet microtubule repeat from LRRC23-KO mouse sperm
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 (mice)

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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: 5.5
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 30 % / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 2137
ExtractionNumber tomograms: 8 / Number images used: 1212 / Software - Name: IMOD (ver. 4.9)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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