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- EMDB-7775: Whole-population, triplet-microtubule map from a Chinese hamster ... -

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Basic information

Entry
Database: EMDB / ID: EMD-7775
TitleWhole-population, triplet-microtubule map from a Chinese hamster ovary (CHO) centriole
Map dataprimary map
Sample
  • Complex: Triplet microtubule from a Chinese Hamster Ovary (CHO) centriole
Biological speciesCricetulus griseus (Chinese hamster)
Methodsubtomogram averaging / cryo EM / Resolution: 25.0 Å
AuthorsAgard DA / Greenan GA
CitationJournal: Elife / Year: 2018
Title: Insights into centriole geometry revealed by cryotomography of doublet and triplet centrioles.
Authors: Garrett A Greenan / Bettina Keszthelyi / Ronald D Vale / David A Agard /
Abstract: Centrioles are cylindrical assemblies comprised of 9 singlet, doublet, or triplet microtubules, essential for the formation of motile and sensory cilia. While the structure of the cilium is being ...Centrioles are cylindrical assemblies comprised of 9 singlet, doublet, or triplet microtubules, essential for the formation of motile and sensory cilia. While the structure of the cilium is being defined at increasing resolution, centriolar structure remains poorly understood. Here, we used electron cryo-tomography to determine the structure of mammalian (triplet) and (doublet) centrioles. Mammalian centrioles have two distinct domains: a 200 nm proximal core region connected by A-C linkers, and a distal domain where the C-tubule is incomplete and a pair of novel linkages stabilize the assembly producing a geometry more closely resembling the ciliary axoneme. centrioles resemble the mammalian core, but with their doublet microtubules linked through the A tubules. The commonality of core-region length, and the abrupt transition in mammalian centrioles, suggests a conserved length-setting mechanism. The unexpected linker diversity suggests how unique centriolar architectures arise in different tissues and organisms.
History
DepositionApr 2, 2018-
Header (metadata) releaseApr 25, 2018-
Map releaseAug 22, 2018-
UpdateAug 22, 2018-
Current statusAug 22, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7775.png

Downloads & links

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Map

FileDownload / File: emd_7775.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.18 Å/pix.
x 150 pix.
= 1227. Å		8.18 Å/pix.
x 150 pix.
= 1227. Å		8.18 Å/pix.
x 150 pix.
= 1227. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.900951 - 1.120925
Average (Standard dev.)0.002345248 (±0.053643465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 1227.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.188.188.18
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z1227.0001227.0001227.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.9011.1210.002

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Supplemental data

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Sample components

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Entire : Triplet microtubule from a Chinese Hamster Ovary (CHO) centriole

EntireName: Triplet microtubule from a Chinese Hamster Ovary (CHO) centriole
Components
  • Complex: Triplet microtubule from a Chinese Hamster Ovary (CHO) centriole

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Supramolecule #1: Triplet microtubule from a Chinese Hamster Ovary (CHO) centriole

SupramoleculeName: Triplet microtubule from a Chinese Hamster Ovary (CHO) centriole
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Cricetulus griseus (Chinese hamster)

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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: 7.2
GridModel: Quantifoil R2/2 / Pretreatment - Type: GLOW DISCHARGE
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 / Average electron dose: 8.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 2300
ExtractionNumber tomograms: 9 / Number images used: 2300
Final angle assignmentType: ANGULAR RECONSTITUTION

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