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- EMDB-5481: Cryo electron tomography of sensory cilia in normal and diseased ... -

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Basic information

Entry
Database: EMDB / ID: EMD-5481
TitleCryo electron tomography of sensory cilia in normal and diseased retinas
Map dataReconstruction of wild type mouse photoreceptor primary cilium
Sample
  • Sample: Wild type mouse photoreceptor primary cilium
  • Organelle or cellular component: Photoreceptor primary cilium
Keywordsphotoreceptor primary cilium / cryo electron tomography / rod outer segment / mouse / cilia / axoneme / retina / photoreceptor
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsGilliam JC / Chang JT / Sandoval IM / Zhang Y / Li T / Pittler SJ / Chiu W / Wensel TG
CitationJournal: Cell / Year: 2012
Title: Three-dimensional architecture of the rod sensory cilium and its disruption in retinal neurodegeneration.
Authors: Jared C Gilliam / Juan T Chang / Ivette M Sandoval / Youwen Zhang / Tiansen Li / Steven J Pittler / Wah Chiu / Theodore G Wensel /
Abstract: Defects in primary cilia lead to devastating disease because of their roles in sensation and developmental signaling but much is unknown about ciliary structure and mechanisms of their formation and ...Defects in primary cilia lead to devastating disease because of their roles in sensation and developmental signaling but much is unknown about ciliary structure and mechanisms of their formation and maintenance. We used cryo-electron tomography to obtain 3D maps of the connecting cilium and adjacent cellular structures of a modified primary cilium, the rod outer segment, from wild-type and genetically defective mice. The results reveal the molecular architecture of the cilium and provide insights into protein functions. They suggest that the ciliary rootlet is involved in cellular transport and stabilizes the axoneme. A defect in the BBSome membrane coat caused defects in vesicle targeting near the base of the cilium. Loss of the proteins encoded by the Cngb1 gene disrupted links between the disk and plasma membranes. The structures of the outer segment membranes support a model for disk morphogenesis in which basal disks are enveloped by the plasma membrane.
History
DepositionAug 23, 2012-
Header (metadata) releaseSep 5, 2012-
Map releaseDec 12, 2012-
UpdateDec 12, 2012-
Current statusDec 12, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
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  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

emd_5481.png

Downloads & links

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Map

FileDownload / File: emd_5481.map.gz / Format: CCP4 / Size: 119.3 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationReconstruction of wild type mouse photoreceptor primary cilium
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
34.93 Å/pix.
x 660 pix.
= 23053.801 Å		34.93 Å/pix.
x 147 pix.
= 5134.71 Å		34.93 Å/pix.
x 660 pix.
= 23053.801 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 34.93 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-5229.0 - 3563.0
Average (Standard dev.)182.502456669999987 (±297.678039549999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin7400
Dimensions147660660
Spacing147660660
CellA: 23053.8 Å / B: 5134.71 Å / C: 23053.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z34.93000151515234.9334.930001515152
M x/y/z660147660
origin x/y/z0.0000.0000.000
length x/y/z23053.8015134.71023053.801
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S123
start NC/NR/NS0740
NC/NR/NS660147660
D min/max/mean-5229.0003563.000182.502

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Supplemental data

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Sample components

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Entire : Wild type mouse photoreceptor primary cilium

EntireName: Wild type mouse photoreceptor primary cilium
Components
  • Sample: Wild type mouse photoreceptor primary cilium
  • Organelle or cellular component: Photoreceptor primary cilium

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Supramolecule #1000: Wild type mouse photoreceptor primary cilium

SupramoleculeName: Wild type mouse photoreceptor primary cilium / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Photoreceptor primary cilium

SupramoleculeName: Photoreceptor primary cilium / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Mus musculus (house mouse) / Strain: C57BL / synonym: mouse / Tissue: retina

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography

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Sample preparation

GridDetails: 200 mesh copper grid with holey carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeJEOL 3200FSC
Specialist opticsEnergy filter - Name: Omega
DateJul 5, 2010
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN / Number real images: 63 / Average electron dose: 90 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal magnification: 25000
Sample stageSpecimen holder: Liquid nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -58 ° / Tilt series - Axis1 - Max angle: 66 ° / Tilt series - Axis1 - Angle increment: 2 °

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Image processing

DetailsStandard IMOD fiducial alignment with weighted back projection
Final reconstructionAlgorithm: OTHER / Software - Name: IMOD / Number images used: 63

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