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- EMDB-2330: Electron cryo-tomography reconstruction and subvolume averaging o... -

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Basic information

Entry
Database: EMDB / ID: EMD-2330
TitleElectron cryo-tomography reconstruction and subvolume averaging of the proximal basal body triplet from Trichonympha
Map dataelectron cryo-tomography reconstruction and subvolume averaging of the proximal basal body triplet from Trichonympha.
Sample
  • Sample: electron cryo-tomography reconstruction and subvolume averaging of the proximal basal body triplet from trichonympha
  • Organelle or cellular component: Basal body
Keywordsmicrotubule triplet / cartwheel / centriole / basal body
Biological speciesTrichonympha (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 42.0 Å
AuthorsGuichard P / Hachet V / Majubu N / Neves A / Demurtas D / Olieric N / Fluckiger I / Yamada A / Kihara K / Nishida Y ...Guichard P / Hachet V / Majubu N / Neves A / Demurtas D / Olieric N / Fluckiger I / Yamada A / Kihara K / Nishida Y / Moriya S / Steinmetz MO / Hongoh Y / Gonczy P
CitationJournal: Curr Biol / Year: 2013
Title: Native architecture of the centriole proximal region reveals features underlying its 9-fold radial symmetry.
Authors: Paul Guichard / Virginie Hachet / Norbert Majubu / Aitana Neves / Davide Demurtas / Natacha Olieric / Isabelle Fluckiger / Akinori Yamada / Kumiko Kihara / Yuichiro Nishida / Shigeharu ...Authors: Paul Guichard / Virginie Hachet / Norbert Majubu / Aitana Neves / Davide Demurtas / Natacha Olieric / Isabelle Fluckiger / Akinori Yamada / Kumiko Kihara / Yuichiro Nishida / Shigeharu Moriya / Michel O Steinmetz / Yuichi Hongoh / Pierre Gönczy /
Abstract: BACKGROUND: Centrioles are cylindrical microtubule-based structures whose assembly is critical for the formation of cilia, flagella, and centrosomes. The centriole proximal region harbors a cartwheel ...BACKGROUND: Centrioles are cylindrical microtubule-based structures whose assembly is critical for the formation of cilia, flagella, and centrosomes. The centriole proximal region harbors a cartwheel that dictates the 9-fold symmetry of centrioles. Although the cartwheel architecture has been recently analyzed, how it connects to the peripheral microtubules is not understood. More generally, a high-resolution view of the proximal region of the centriole is lacking, thus limiting understanding of the underlying assembly mechanisms.
RESULTS: We report the complete architecture of the Trichonympha centriole proximal region using cryotomography. The resulting 3D map reveals several features, including additional densities in the ...RESULTS: We report the complete architecture of the Trichonympha centriole proximal region using cryotomography. The resulting 3D map reveals several features, including additional densities in the cartwheel that exhibit a 9-fold symmetrical arrangement, as well as the structure of the Pinhead and the A-C linker that connect to microtubules. Moreover, we uncover striking chiral features that might impart directionality to the entire centriole. Furthermore, we identify Trichonympha SAS-6 and demonstrate that it localizes to the cartwheel in vivo.
CONCLUSIONS: Our work provides unprecedented insight into the architecture of the centriole proximal region, which is key for a thorough understanding of the mechanisms governing centriole assembly.
History
DepositionMar 11, 2013-
Header (metadata) releaseApr 10, 2013-
Map releaseAug 21, 2013-
UpdateSep 25, 2013-
Current statusSep 25, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.370940815
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2330.png

Downloads & links

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Map

FileDownload / File: emd_2330.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationelectron cryo-tomography reconstruction and subvolume averaging of the proximal basal body triplet from Trichonympha.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.5 Å/pix.
x 66 pix.
= 495. Å		7.5 Å/pix.
x 124 pix.
= 930. Å		7.5 Å/pix.
x 111 pix.
= 832.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 7.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.0 / Movie #1: 0.4
Minimum - Maximum-3.1838901 - 2.45359182
Average (Standard dev.)-0.90669858 (±0.93229675)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions12411166
Spacing12411166
CellA: 832.5 Å / B: 930.0 Å / C: 495.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.57.57.5
M x/y/z11112466
origin x/y/z0.0000.0000.000
length x/y/z832.500930.000495.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-27-15-36
NX/NY/NZ553173
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS11112466
D min/max/mean-3.1842.454-0.907

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Supplemental data

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Sample components

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Entire : electron cryo-tomography reconstruction and subvolume averaging o...

EntireName: electron cryo-tomography reconstruction and subvolume averaging of the proximal basal body triplet from trichonympha
Components
  • Sample: electron cryo-tomography reconstruction and subvolume averaging of the proximal basal body triplet from trichonympha
  • Organelle or cellular component: Basal body

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Supramolecule #1000: electron cryo-tomography reconstruction and subvolume averaging o...

SupramoleculeName: electron cryo-tomography reconstruction and subvolume averaging of the proximal basal body triplet from trichonympha
type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Basal body

SupramoleculeName: Basal body / type: organelle_or_cellular_component / ID: 1 / Name.synonym: centriole / Recombinant expression: No
Source (natural)Organism: Trichonympha (eukaryote) / Organelle: centriole / Location in cell: cytoplasmic

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2 / Details: K-Pipes 10 mM
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Method: Blot for 1 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI 20
DateJul 1, 2012
Image recordingNumber real images: 100
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 29000
Sample stageSpecimen holder model: OTHER / Tilt series - Axis1 - Min angle: -65 ° / Tilt series - Axis1 - Max angle: 65 °

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 42.0 Å / Resolution method: OTHER / Software - Name: IMOD, Spider, Bsoft / Number subtomograms used: 600

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