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- EMDB-38004: consensus map of RS head-neck monomer complex -

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Basic information

Entry
Database: EMDB / ID: EMD-38004
Titleconsensus map of RS head-neck monomer complex
Map datasharpened consensus map of RS head-neck monomer
Sample
  • Complex: RS head-neck complex
KeywordsRadial spoke / cilia / axoneme / STRUCTURAL PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsMeng X / Cong Y
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
DepositionNov 9, 2023-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateFeb 7, 2024-
Current statusFeb 7, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38004.png

Downloads & links

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Map

FileDownload / File: emd_38004.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened consensus map of RS head-neck monomer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 560 pix.
= 478.24 Å		0.85 Å/pix.
x 560 pix.
= 478.24 Å		0.85 Å/pix.
x 560 pix.
= 478.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.854 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.0017886363 - 1.7459441
Average (Standard dev.)0.00028050249 (±0.0122720525)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 478.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpening consensus map of RS head-neck monomer

Fileemd_38004_additional_1.map
AnnotationUnsharpening consensus map of RS head-neck monomer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A for consensus map of RS head-neck monomer

Fileemd_38004_half_map_1.map
Annotationhalf map A for consensus map of RS head-neck monomer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B for consensus map of RS head-neck monomer

Fileemd_38004_half_map_2.map
Annotationhalf map B for consensus map of RS head-neck monomer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RS head-neck complex

EntireName: RS head-neck complex
Components
  • Complex: RS head-neck complex

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Supramolecule #1: RS head-neck complex

SupramoleculeName: RS head-neck complex / type: complex / 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
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
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: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 433940
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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