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- EMDB-9168: Electron cryo-tomography and subtomogram averaging of microtubule... -

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Basic information

Entry
Database: EMDB / ID: EMD-9168
TitleElectron cryo-tomography and subtomogram averaging of microtubule triplet from procentriole
Map dataA subtomogram average of the A-tubule in procentriole from Chlamydomonas Reinhardtii
Sample
  • Organelle or cellular component: Centriole
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 21.4 Å
AuthorsLi S / Fernandez JJ / Marshall W / Agard DA
Funding support United States, European Union, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM031627 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM118099 United States
European Union (EU)SAF2017-84565-REuropean Union
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.
History
DepositionOct 1, 2018-
Header (metadata) releaseOct 24, 2018-
Map releaseFeb 27, 2019-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.87
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.87
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9168.png

Downloads & links

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Map

FileDownload / File: emd_9168.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA subtomogram average of the A-tubule in procentriole from Chlamydomonas Reinhardtii
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.87 / Movie #1: 2.87
Minimum - Maximum-12.439011 - 17.552008
Average (Standard dev.)0.045318108 (±1.4927415)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin111
Dimensions120120120
Spacing120120120
CellA=B=C: 578.4 Å
α=β=γ: 90.0 °

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/NZ-51-35-11
NX/NY/NZ11110799
MAP C/R/S123
start NC/NR/NS111
NC/NR/NS120120120
D min/max/mean-12.43917.5520.045

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Supplemental data

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Sample components

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Entire : Centriole

EntireName: Centriole
Components
  • Organelle or cellular component: Centriole

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Supramolecule #1: Centriole

SupramoleculeName: Centriole / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Details: isolated centriole and procentriole
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC849

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-5 / Average exposure time: 1.0 sec. / Average electron dose: 0.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 21.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 12517
ExtractionNumber tomograms: 193 / Number images used: 12937
Final angle assignmentType: MAXIMUM LIKELIHOOD
Crystal parametersUnit cell - A: 578.4 Å / Unit cell - B: 578.4 Å / Unit cell - C: 578.4 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Space group: C1

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