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- EMDB-45689: The Outer Dynein Arm-Docking Complex (ODA-DC) from bovine Fallopi... -

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Basic information

Entry
Database: EMDB / ID: EMD-45689
TitleThe Outer Dynein Arm-Docking Complex (ODA-DC) from bovine Fallopian tube
Map data
Sample
  • Organelle or cellular component: cilia from bovine Fallopian tube
Keywordsaxoneme / cilia / microtubule / dynein / Fallopian tube / doublet microtubule (DMT) / sperm / STRUCTURAL PROTEIN
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsSun C / Zhang R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM138854 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
DepositionJul 11, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45689.png

Downloads & links

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Map

FileDownload / File: emd_45689.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 512 pix.
= 686.08 Å		1.34 Å/pix.
x 512 pix.
= 686.08 Å		1.34 Å/pix.
x 512 pix.
= 686.08 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
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Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.423311 - 0.83479476
Average (Standard dev.)0.002951901 (±0.058245383)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 686.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45689_msk_1.map
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Additional map: #1

Fileemd_45689_additional_1.map
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Half map: #1

Fileemd_45689_half_map_1.map
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Half map: #2

Fileemd_45689_half_map_2.map
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Sample components

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Entire : cilia from bovine Fallopian tube

EntireName: cilia from bovine Fallopian tube
Components
  • Organelle or cellular component: cilia from bovine Fallopian tube

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Supramolecule #1: cilia from bovine Fallopian tube

SupramoleculeName: cilia from bovine Fallopian tube / type: organelle_or_cellular_component / ID: 1 / Parent: 0
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: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN 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

Startup modelType of model: EMDB MAP
EMDB ID:

40619

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 95292
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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