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- EMDB-2094: Central hub structure of Trichonympha cartwheel -

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Basic information

Entry
Database: EMDB / ID: EMD-2094
TitleCentral hub structure of Trichonympha cartwheel
Map dataReconstruction of the central hub (cartwheel component)
Sample
  • Sample: Trichonympha central hub, central part of the Basal body cartwheel
  • Organelle or cellular component: Centriole
Keywordscentriole / cartwheel / basal body
Biological speciesTrichonympha (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 45.0 Å
AuthorsGuichard P / Desfosses A / Maheshwari A / Hachet V / Dietrich C / Brune A / Ishikawa T / Sachse C / Gonczy P
CitationJournal: Science / Year: 2012
Title: Cartwheel architecture of Trichonympha basal body.
Authors: Paul Guichard / Ambroise Desfosses / Aditi Maheshwari / Virginie Hachet / Carsten Dietrich / Andreas Brune / Takashi Ishikawa / Carsten Sachse / Pierre Gönczy /
Abstract: Centrioles and basal bodies are essential for the formation of cilia, flagella, and centrosomes. They exhibit a characteristic ninefold symmetry imparted by a cartwheel thought to contain rings of ...Centrioles and basal bodies are essential for the formation of cilia, flagella, and centrosomes. They exhibit a characteristic ninefold symmetry imparted by a cartwheel thought to contain rings of SAS-6 proteins. We used cryoelectron tomography to investigate the architecture of the exceptionally long cartwheel of the flagellate Trichonympha. We found that the cartwheel is a stack of central rings that exhibit a vertical periodicity of 8.5 nanometers and is able to accommodate nine SAS-6 homodimers. The spokes that emanate from two such rings associate into a layer, with a vertical periodicity of 17 nanometers on the cartwheel margin. Thus, by using the power of biodiversity, we unveiled the architecture of the cartwheel at the root of the ninefold symmetry of centrioles and basal bodies.
History
DepositionMay 8, 2012-
Header (metadata) releaseSep 19, 2012-
Map releaseSep 19, 2012-
UpdateSep 26, 2012-
Current statusSep 26, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2094.png

Downloads & links

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Map

FileDownload / File: emd_2094.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the central hub (cartwheel component)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.07 Å/pix.
x 100 pix.
= 707. Å		7.07 Å/pix.
x 100 pix.
= 707. Å		7.07 Å/pix.
x 100 pix.
= 707. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.02
Minimum - Maximum-0.05694 - 0.06882826
Average (Standard dev.)0.00019145 (±0.01341766)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 707.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.077.077.07
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z707.000707.000707.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ128128168
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-0.0570.0690.000

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Supplemental data

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Sample components

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Entire : Trichonympha central hub, central part of the Basal body cartwheel

EntireName: Trichonympha central hub, central part of the Basal body cartwheel
Components
  • Sample: Trichonympha central hub, central part of the Basal body cartwheel
  • Organelle or cellular component: Centriole

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Supramolecule #1000: Trichonympha central hub, central part of the Basal body cartwheel

SupramoleculeName: Trichonympha central hub, central part of the Basal body cartwheel
type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Centriole

SupramoleculeName: Centriole / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Basal body / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Trichonympha (eukaryote) / Organelle: Basal body

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging

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Sample preparation

BufferDetails: K-Pipes 10 mM
VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 2200FS
DateJul 1, 2011
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

Details414 original images (before symmetrization) were included in the final reconstruction. Average number of tilts used in the 3D reconstructions: 414.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 45.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN, himpose, SPIDER

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Atomic model buiding 1

Initial modelPDB ID:

3q0x

SoftwareName: Chimera
RefinementSpace: REAL

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