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- EMDB-3786: Cryo-electron tomography averaged map of microtubule doublet from... -

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Basic information

Entry
Database: EMDB / ID: 3786
TitleCryo-electron tomography averaged map of microtubule doublet from p23 mutant Chlamydomonas axoneme
Map dataSubaverage after subtomogram classification of Chlamydomonas pf23 cilia, based on outer dynein arm structure
SampleCiliary microtubule doublet with dynein, radial spokes and other binding proteins:
SourceChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / 50 Å resolution
AuthorsSale WS / Ishikawa T / Yamamoto R / Obbineni JM / Alford LM / Hwang J / Ide T / Owa M / Kon T / Inaba K / Noliyanda J / King SM / Dutcher S
CitationJournal: PLoS Genet. / Year: 2017
Title: Chlamydomonas DYX1C1/PF23 is essential for axonemal assembly and proper morphology of inner dynein arms.
Authors: Ryosuke Yamamoto / Jagan M Obbineni / Lea M Alford / Takahiro Ide / Mikito Owa / Juyeon Hwang / Takahide Kon / Kazuo Inaba / Noliyanda James / Stephen M King / Takashi Ishikawa / Winfield S Sale / Susan K Dutcher
DateDeposition: Jul 6, 2017 / Header (metadata) release: Aug 16, 2017 / Map release: Sep 6, 2017 / Last update: Sep 20, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: -0.28
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: -0.28
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3786.map.gz (map file in CCP4 format, 49949 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
232 pix
5.68 Å/pix.
= 1317.76 Å
232 pix
5.68 Å/pix.
= 1317.76 Å
232 pix
5.68 Å/pix.
= 1317.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.68 Å
Density
Contour Level:0.001 (by author), -0.28 (movie #1):
Minimum - Maximum-0.76053894 - 0.66737646
Average (Standard dev.)-0.00049874233 (0.098439604)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions232232232
Origin000
Limit231231231
Spacing232232232
CellA=B=C: 1317.76 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.685.685.68
M x/y/z232232232
origin x/y/z0.0000.0000.000
length x/y/z1317.7601317.7601317.760
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS232232232
D min/max/mean-0.7610.667-0.000

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Supplemental data

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Sample components

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Entire Ciliary microtubule doublet with dynein, radial spokes and other ...

EntireName: Ciliary microtubule doublet with dynein, radial spokes and other binding proteins
Number of components: 1

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Component #1: cellular-component, Ciliary microtubule doublet with dynein, radi...

Cellular-componentName: Ciliary microtubule doublet with dynein, radial spokes and other binding proteins
Recombinant expression: No
SourceSpecies: Chlamydomonas reinhardtii (plant) / Strain: pf23
Source (natural)Organelle: cilia

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Experimental details

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Sample preparation

SpecimenSpecimen state: cell / Method: cryo EM
Sample solutionBuffer solution: 30 mM HEPES, 5 mM MgSO4, 1 mM DTT, 1 mM EGTA, and 50 mM potassium acetate, pH7.4
pH: 7.4
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 70 % / Details: one side blotting

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 0.8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 20000 X (nominal) / Imaging mode: BRIGHT FIELD / Energy filter: JEOL in-column / Energy window: 0-25 eV
Specimen HolderModel: GATAN LIQUID NITROGEN / Tilt Angle: -60 - 60 deg.
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging
3D reconstructionAlgorithm: BACK PROJECTION / Software: SPIDER / Resolution: 50 Å / Resolution method: OTHER
Details: Visual estimation, compared with datasets in the past
Euler angles: 3D cross correlation by Spider

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