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- EMDB-8537: Cryo-EM structure of 48nm repeat ciliary microtubule doublet -

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Basic information

Database: EMDB / ID: 8537
TitleCryo-EM structure of 48nm repeat ciliary microtubule doublet
Sample48nm-repeat of microtubule doublet
SourceTetrahymena thermophila / eukaryote
Map data48nm repeat map of the doublet from Tetrahymena thermophila
Methodsingle particle reconstruction, at 8.6 Å resolution
AuthorsIchikawa M / Liu D / Kastritis PL / Basu K / Bui KH
CitationNat Commun, 2017, 8, 15035-15035

Nat Commun, 2017, 8, 15035-15035 Yorodumi Papers
Subnanometre-resolution structure of the doublet microtubule reveals new classes of microtubule-associated proteins.
Muneyoshi Ichikawa / Dinan Liu / Panagiotis L Kastritis / Kaustuv Basu / Tzu Chin Hsu / Shunkai Yang / Khanh Huy Bui

DateDeposition: Dec 22, 2016 / Header (metadata) release: Jan 18, 2017 / Map release: May 10, 2017 / Last update: Feb 14, 2018

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_8537.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
2.75 Å/pix.
= 704. Å
256 pix
2.75 Å/pix.
= 704. Å
256 pix
2.75 Å/pix.
= 704. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.75 Å
Contour Level:0.025 (by author), 0.05 (movie #1):
Minimum - Maximum-0.16210996 - 0.2697493
Average (Standard dev.)0.001460734 (0.036109127)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 704 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.752.752.75
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z704.000704.000704.000
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.1620.2700.001

Supplemental data

Sample components

Entire 48nm-repeat of microtubule doublet

EntireName: 48nm-repeat of microtubule doublet / Number of components: 1

Component #1: cellular-component, 48nm-repeat of microtubule doublet

Cellular-componentName: 48nm-repeat of microtubule doublet / Recombinant expression: No
SourceSpecies: Tetrahymena thermophila / eukaryote / Strain: SB255
Source (natural)Organelle: cilia / Location in cell: cilia

Experimental details

Sample preparation

Specimen statefilament
Sample solutionSpecimen conc.: 2 mg/ml / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 100 % / Details: Blot force 3 for 5 seconds

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 3800 nm
CameraDetector: FEI FALCON II (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 5983

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 15697
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 8.6 Å / Resolution method: FSC 0.143 CUT-OFF

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