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- EMDB-37111: 48-nm repeat DMT -

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Basic information

Entry
Database: EMDB / ID: EMD-37111
Title48-nm repeat DMT
Map data
Sample
  • Organelle or cellular component: The ependymal cilia
Keywordsmotile cilia / axoneme / sub-tomogram average / doublet microtubule / STRUCTURAL PROTEIN
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 19.6 Å
AuthorsCong X / Yao C
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2024
Title: Multi-scale structures of the mammalian radial spoke and divergence of axonemal complexes in ependymal cilia.
Authors: Xueming Meng / Cong Xu / Jiawei Li / Benhua Qiu / Jiajun Luo / Qin Hong / Yujie Tong / Chuyu Fang / Yanyan Feng / Rui Ma / Xiangyi Shi / Cheng Lin / Chen Pan / Xueliang Zhu / Xiumin Yan / Yao Cong /
Abstract: Radial spokes (RS) transmit mechanochemical signals between the central pair (CP) and axonemal dynein arms to coordinate ciliary motility. Atomic-resolution structures of metazoan RS and structures ...Radial spokes (RS) transmit mechanochemical signals between the central pair (CP) and axonemal dynein arms to coordinate ciliary motility. Atomic-resolution structures of metazoan RS and structures of axonemal complexes in ependymal cilia, whose rhythmic beating drives the circulation of cerebrospinal fluid, however, remain obscure. Here, we present near-atomic resolution cryo-EM structures of mouse RS head-neck complex in both monomer and dimer forms and reveal the intrinsic flexibility of the dimer. We also map the genetic mutations related to primary ciliary dyskinesia and asthenospermia on the head-neck complex. Moreover, we present the cryo-ET and sub-tomogram averaging map of mouse ependymal cilia and build the models for RS1-3, IDAs, and N-DRC. Contrary to the conserved RS structure, our cryo-ET map reveals the lack of IDA-b/c/e and the absence of Tektin filaments within the A-tubule of doublet microtubules in ependymal cilia compared with mammalian respiratory cilia and sperm flagella, further exemplifying the structural diversity of mammalian motile cilia. Our findings shed light on the stepwise mammalian RS assembly mechanism, the coordinated rigid and elastic RS-CP interaction modes beneficial for the regulation of asymmetric ciliary beating, and also facilitate understanding on the etiology of ciliary dyskinesia-related ciliopathies and on the ependymal cilia in the development of hydrocephalus.
History
DepositionAug 8, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37111.png

Downloads & links

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Map

FileDownload / File: emd_37111.map.gz / Format: CCP4 / Size: 125 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.)
2.7 Å/pix.
x 320 pix.
= 864. Å		2.7 Å/pix.
x 320 pix.
= 864. Å		2.7 Å/pix.
x 320 pix.
= 864. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.61049044 - 0.85822684
Average (Standard dev.)0.012850788 (±0.075812526)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 864.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37111_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_37111_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : The ependymal cilia

EntireName: The ependymal cilia
Components
  • Organelle or cellular component: The ependymal cilia

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Supramolecule #1: The ependymal cilia

SupramoleculeName: The ependymal cilia / type: organelle_or_cellular_component / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 19.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1574
ExtractionNumber tomograms: 14 / Number images used: 788
Final angle assignmentType: MAXIMUM LIKELIHOOD

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