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- EMDB-2119: Cryo-electron tomography averaged map of microtubule doublet 1 in... -

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Basic information

Entry
Database: EMDB / ID: 2119
TitleCryo-electron tomography averaged map of microtubule doublet 1 in the proximal region of Chlamydomonas axoneme
Keywordsaxoneme / dynein / Chlamydomonas / microtubule doublet
SampleOuter doublet 1 of Chlamydomonas axoneme in the proximal region
SourceChlamydomonas reinhardtii / plant / green algae
Map dataReconstruction of outer doublet 1 of the Chlamydomonas axoneme in the proximal region.
Methodsubtomogram averaging, at 44 A resolution
AuthorsBui KH / Yagi T / Yamamoto R / Kamiya R / Ishikawa T
CitationJ. Cell Biol., 2012, 198, 913-925

J. Cell Biol., 2012, 198, 913-925 StrPapers
Polarity and asymmetry in the arrangement of dynein and related structures in the Chlamydomonas axoneme.
Khanh Huy Bui / Toshiki Yagi / Ryosuke Yamamoto / Ritsu Kamiya / Takashi Ishikawa

DateDeposition: Jun 11, 2012 / Header (metadata) release: Jun 14, 2012 / Map release: Sep 12, 2012 / Last update: Jun 11, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.8
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.8
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_2119.map.gz (map file in CCP4 format, 31251 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
7.25 A/pix
= 1450. A
200 pix
7.25 A/pix
= 1450. A
200 pix
7.25 A/pix
= 1450. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 7.25 A
Density
Contour Level:0.8 (by author), 0.8 (movie #1):
Minimum - Maximum-6.91151142 - 9.06010532
Average (Standard dev.)6E-8 (1.00000012)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
CellA=B=C: 1450 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z7.257.257.25
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z1450.0001450.0001450.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-6.9129.0600.000

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Supplemental data

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Sample components

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Entire Outer doublet 1 of Chlamydomonas axoneme in the proximal region

EntireName: Outer doublet 1 of Chlamydomonas axoneme in the proximal region
Details: Flagella were isolated from Chlamydomonas. / Number of components: 1

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Component #1: cellular-component, flagellum

Cellular-componentName: flagellum / a.k.a: axoneme,cilia / Recombinant expression: No
SourceSpecies: Chlamydomonas reinhardtii / plant / green algae / Strain: c137 (mt+)
Source (natural)Organelle: flagella / Location in cell: proximal part of the flagellum

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Experimental details

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Sample preparation

Sample solutionSpecimen conc.: 2 mg/ml
Buffer solution: 30 mM Hepes, pH 7.4, 5 mM MgSO4, 1 mM DTT, 0.5 mM EDTA, 25 mM KCl, and 0.5% (wt/vol) polyethylene glycol (MW 20,000)
pH: 7.4
Support film300 mesh Quantifoil Holey Carbon copper grid R2/1
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 110 K / Humidity: 90 % / Method: Offset -3, blot 3 seconds, drain time 0 second

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20 / Date: Nov 26, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 60 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 27500 X (nominal), 19303 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 4000 - 6000 nm / Energy filter: Gatan Tridem / Energy window: 0-20 eV
Specimen HolderHolder: Gatan 626, liquid nitrogen cooled / Model: GATAN LIQUID NITROGEN / Tilt Angle: -60 - 60 deg. / Temperature: 98 K ( 93 - 118 K)
CameraDetector: GATAN ULTRASCAN 1000 (2k x 2k)

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Image acquisition

Image acquisitionNumber of digital images: 499 / Bit depth: 16

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Image processing

ProcessingMethod: subtomogram averaging
Details: R-weighted back projection using IMOD with fiducial markers. Average number of tilts used in the 3D reconstructions: 61. Average tomographic tilt angle increment: 2.
3D reconstructionAlgorithm: subtomogram averaging / Software: IMOD, BSOFT, SPIDER, TOM, package, Matlab / Resolution: 44 A / Resolution method: FSC 0.5

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