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- EMDB-9171: Electron cryo-tomography and subtomogram averaging of microtubule... -

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Entry
Database: EMDB / ID: 9171
TitleElectron cryo-tomography and subtomogram averaging of microtubule triplet from procentriole
Map datasubtomogram average of the pinhead associated with the A-tubule in procentriole from Chlamydomonas reinhardtii
SampleCentriole:
SourceChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / 23.1 Å resolution
AuthorsLi S / Fernandez JJ / Marshall W / Agard DA
CitationJournal: Elife / Year: 2019
Title: Electron cryo-tomography provides insight into procentriole architecture and assembly mechanism.
Authors: Sam Li / Jose-Jesus Fernandez / Wallace F Marshall / David A Agard
Abstract: Centriole is an essential structure with multiple functions in cellular processes. Centriole biogenesis and homeostasis is tightly regulated. Using electron cryo-tomography (cryoET) we present the ...Centriole is an essential structure with multiple functions in cellular processes. Centriole biogenesis and homeostasis is tightly regulated. Using electron cryo-tomography (cryoET) we present the structure of procentrioles from . We identified a set of non-tubulin components attached to the triplet microtubule (MT), many are at the junctions of tubules likely to reinforce the triplet. We describe structure of the A-C linker that bridges neighboring triplets. The structure infers that POC1 is likely an integral component of A-C linker. Its conserved WD40 β-propeller domain provides attachment sites for other A-C linker components. The twist of A-C linker results in an iris diaphragm-like motion of the triplets in the longitudinal direction of procentriole. Finally, we identified two assembly intermediates at the growing ends of procentriole allowing us to propose a model for the procentriole assembly. Our results provide a comprehensive structural framework for understanding the molecular mechanisms underpinning procentriole biogenesis and assembly.
DateDeposition: Oct 1, 2018 / Header (metadata) release: Oct 24, 2018 / Map release: Feb 27, 2019 / Last update: Feb 27, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.95
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2.95
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

Fileemd_9171.map.gz (map file in CCP4 format, 6913 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
120 pix
4.82 Å/pix.
= 578.4 Å
120 pix
4.82 Å/pix.
= 578.4 Å
120 pix
4.82 Å/pix.
= 578.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.82 Å
Density
Contour Level:2.95 (by author), 2.95 (movie #1):
Minimum - Maximum-18.101343 - 22.958539999999999
Average (Standard dev.)0.023905491 (1.2265933)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions120120120
Origin1.01.01.0
Limit120.0120.0120.0
Spacing120120120
CellA=B=C: 578.4 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.824.824.82
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z578.400578.400578.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ364364364
MAP C/R/S123
start NC/NR/NS111
NC/NR/NS120120120
D min/max/mean-18.10122.9590.024

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Supplemental data

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Sample components

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Entire Centriole

EntireName: Centriole / Details: isolated centriole and procentriole / Number of components: 1

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Component #1: cellular-component, Centriole

Cellular-componentName: Centriole / Details: isolated centriole and procentriole / Recombinant expression: No
SourceSpecies: Chlamydomonas reinhardtii (plant) / Strain: CC849

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Experimental details

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Sample preparation

SpecimenSpecimen state: cell / Method: cryo EM
Crystal parametersSpace group: C1 / A: 578.4 Å / B: 578.4 Å / C: 578.4 Å / Alpha: 90 deg. / Beta: 90 deg. / Gamma: 90 deg.
Sample solutionpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 0.6 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionSampling size: 5 microns

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Image processing

ProcessingMethod: subtomogram averaging / Number of subtomograms: 4763
3D reconstructionResolution: 23.1 Å / Resolution method: FSC 0.143 CUT-OFF

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