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- EMDB-41812: Subtomogram Averaging of the Triplet from Mouse Centrioles -

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Basic information

Entry
Database: EMDB / ID: EMD-41812
TitleSubtomogram Averaging of the Triplet from Mouse Centrioles
Map dataSubtomogram averaging of complete triplet from proximal centriole
Sample
  • Organelle or cellular component: ROS(rod of outer segments)of mouse photoreceptor
KeywordsInhibitor / SIGNALING PROTEIN
Biological speciesMus (mice)
Methodsubtomogram averaging / cryo EM / Resolution: 40.0 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_41812.png

Downloads & links

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Map

FileDownload / File: emd_41812.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram averaging of complete triplet from proximal centriole
Voxel sizeX=Y=Z: 4.45 Å
Density
Contour LevelBy AUTHOR: 1.8
Minimum - Maximum-10.211536000000001 - 9.634971999999999
Average (Standard dev.)0.09967119 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 1139.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Subtomogram averaging of incomplete triplet from middle centriole

Fileemd_41812_additional_1.map
AnnotationSubtomogram averaging of incomplete triplet from middle centriole
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Subtomogram averaging of doublets from distal centriole

Fileemd_41812_additional_2.map
AnnotationSubtomogram averaging of doublets from distal centriole
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Subtomogram averaging of doublets from connecting cilium

Fileemd_41812_additional_3.map
AnnotationSubtomogram averaging of doublets from connecting cilium
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Masked odd half map

Fileemd_41812_half_map_1.map
AnnotationMasked odd half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Masked even half map

Fileemd_41812_half_map_2.map
AnnotationMasked even half 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 (mice)

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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
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.8 µm
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
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 15 / Number images used: 1800
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 40.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1800
FSC plot (resolution estimation)

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