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- EMDB-53135: native axonemal doublet microtubule from bovine sperm, 96-nm repe... -

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Basic information

Entry
Database: EMDB / ID: EMD-53135
Titlenative axonemal doublet microtubule from bovine sperm, 96-nm repeat (consensus refinement, microtubule-centered)
Map datamain map, unmasked, unsharpened
Sample
  • Organelle or cellular component: 96-nm repeat of axonemal doublet microtubules from bovine sperm
Keywordsaxoneme / cilia / microtubule / dynein / sperm / STRUCTURAL PROTEIN
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLeung MR / Sun C / Zeng J / Anderson JR / Niu Q / Huang W / Noteborn WEM / Brown A / Zeev-Ben-Mordehai T / Zhang R
Funding support Netherlands, United States, 4 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)OCENW.XL21.XL21.048 Netherlands
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM138854 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM141109 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM143183 United States
CitationJournal: Nature / Year: 2025
Title: Structural diversity of axonemes across mammalian motile cilia.
Authors: Miguel Ricardo Leung / Chen Sun / Jianwei Zeng / Jacob R Anderson / Qingwei Niu / Wei Huang / Willem E M Noteborn / Alan Brown / Tzviya Zeev-Ben-Mordehai / Rui Zhang /
Abstract: Reproduction, development and homeostasis depend on motile cilia, whose rhythmic beating is powered by a microtubule-based molecular machine called the axoneme. Although an atomic model of the ...Reproduction, development and homeostasis depend on motile cilia, whose rhythmic beating is powered by a microtubule-based molecular machine called the axoneme. Although an atomic model of the axoneme is available for the alga Chlamydomonas reinhardtii, structures of mammalian axonemes are incomplete. Furthermore, we do not fully understand how molecular structures of axonemes vary across motile-ciliated cell types in the body. Here we use cryoelectron microscopy, cryoelectron tomography and proteomics to resolve the 96-nm modular repeat of axonemal doublet microtubules (DMTs) from both sperm flagella and epithelial cilia of the oviduct, brain ventricles and respiratory tract. We find that sperm DMTs are the most specialized, with epithelial cilia having only minor differences across tissues. We build a model of the mammalian sperm DMT, defining the positions and interactions of 181 proteins including 34 newly identified proteins. We elucidate the composition of radial spoke 3 and uncover binding sites of kinases associated with regeneration of ATP and regulation of ciliary motility. We discover a sperm-specific, axoneme-tethered T-complex protein ring complex (TRiC) chaperone that may contribute to construction or maintenance of the long flagella of mammalian sperm. We resolve axonemal dyneins in their prestroke states, illuminating conformational changes that occur during ciliary movement. Our results illustrate how elements of chemical and mechanical regulation are embedded within the axoneme, providing valuable resources for understanding the aetiology of ciliopathy and infertility, and exemplifying the discovery power of modern structural biology.
History
DepositionMar 13, 2025-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53135.png

Downloads & links

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Map

FileDownload / File: emd_53135.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map, unmasked, unsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 512 pix.
= 666.214 Å		1.3 Å/pix.
x 512 pix.
= 666.214 Å		1.3 Å/pix.
x 512 pix.
= 666.214 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3012 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.9930661 - 2.0910184
Average (Standard dev.)0.013458287 (±0.1541942)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 666.2144 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half-map 1

Fileemd_53135_half_map_1.map
Annotationhalf-map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 2

Fileemd_53135_half_map_2.map
Annotationhalf-map 2
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 96-nm repeat of axonemal doublet microtubules from bovine sperm

EntireName: 96-nm repeat of axonemal doublet microtubules from bovine sperm
Components
  • Organelle or cellular component: 96-nm repeat of axonemal doublet microtubules from bovine sperm

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Supramolecule #1: 96-nm repeat of axonemal doublet microtubules from bovine sperm

SupramoleculeName: 96-nm repeat of axonemal doublet microtubules from bovine sperm
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#479
Source (natural)Organism: Bos taurus (domestic cattle)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.9
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2585140
Startup modelType of model: EMDB MAP
EMDB ID:

24664

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 203560
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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