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- EMDB-41814: Subtomogram averaging of ciliary beads from ciliary membrane -

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Basic information

Entry
Database: EMDB / ID: EMD-41814
TitleSubtomogram averaging of ciliary beads from ciliary membrane
Map dataSubtomogram averaging of ciliary beads from ciliary membrane
Sample
  • Organelle or cellular component: ROS(rod of outer segments)of mouse photoreceptor
KeywordsInhibitor / SIGNALING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 55.0 Å
AuthorsZhang Z / Moye A / He F / Chen M / Agosto AA / Wensel TG
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01-EY026545, R01-EY031949, F32-EY-031574, and the Welch Foundation (Q0035) United States
CitationJournal: Life Sci Alliance / Year: 2024
Title: Centriole and transition zone structures in photoreceptor cilia revealed by cryo-electron tomography.
Authors: Zhixian Zhang / Abigail R Moye / Feng He / Muyuan Chen / Melina A Agosto / Theodore G Wensel /
Abstract: Primary cilia mediate sensory signaling in multiple organisms and cell types but have structures adapted for specific roles. Structural defects in them lead to devastating diseases known as ...Primary cilia mediate sensory signaling in multiple organisms and cell types but have structures adapted for specific roles. Structural defects in them lead to devastating diseases known as ciliopathies in humans. Key to their functions are structures at their base: the basal body, the transition zone, the "Y-shaped links," and the "ciliary necklace." We have used cryo-electron tomography with subtomogram averaging and conventional transmission electron microscopy to elucidate the structures associated with the basal region of the "connecting cilia" of rod outer segments in mouse retina. The longitudinal variations in microtubule (MT) structures and the lumenal scaffold complexes connecting them have been determined, as well as membrane-associated transition zone structures: Y-shaped links connecting MT to the membrane, and ciliary beads connected to them that protrude from the cell surface and form a necklace-like structure. These results represent a clearer structural scaffold onto which molecules identified by genetics, proteomics, and superresolution fluorescence can be placed in our emerging model of photoreceptor sensory cilia.
History
DepositionSep 1, 2023-
Header (metadata) releaseJan 3, 2024-
Map releaseJan 3, 2024-
UpdateJan 24, 2024-
Current statusJan 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41814.png

Downloads & links

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Map

FileDownload / File: emd_41814.map.gz / Format: CCP4 / Size: 12.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram averaging of ciliary beads from ciliary membrane
Voxel sizeX=Y=Z: 4.45 Å
Density
Contour LevelBy AUTHOR: 1.3
Minimum - Maximum-6.1500235 - 8.507955000000001
Average (Standard dev.)0.20996617 (±0.9999998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions148148148
Spacing148148148
CellA=B=C: 658.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Masked even half map

Fileemd_41814_half_map_1.map
AnnotationMasked even half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Masked odd map

Fileemd_41814_half_map_2.map
AnnotationMasked odd map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ROS(rod of outer segments)of mouse photoreceptor

EntireName: ROS(rod of outer segments)of mouse photoreceptor
Components
  • Organelle or cellular component: ROS(rod of outer segments)of mouse photoreceptor

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Supramolecule #1: ROS(rod of outer segments)of mouse photoreceptor

SupramoleculeName: ROS(rod of outer segments)of mouse photoreceptor / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: DIRECT ELECTRON DE-12 (4k x 3k) / Average exposure time: 1.0 sec. / Average electron dose: 10.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 55.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 400
ExtractionNumber tomograms: 1 / Number images used: 500
Final angle assignmentType: PROJECTION MATCHING

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