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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: Guichard P / Desfosses A / Maheshwari A / Hachet V / Dietrich C / Brune A / Ishikawa T / Sachse C / Gonczy P
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

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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)
Voxel sizeX=Y=Z: 7.07 Å
Density
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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