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- EMDB-5330: Cryo-electron tomography reveals novel interactions and doublet-s... -

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Basic information

Entry
Database: EMDB / ID: 5330
TitleCryo-electron tomography reveals novel interactions and doublet-specific structures in the I1 dynein
Keywordsaxoneme / molecular motor / motility regulation / flagella
SampleCryo-electron tomography and subtomographic average (750 axonemal repeats) of isolated axonemes of wild type Chlamydomonas (CC 125, 137c), I1 dynein complex (dynein f) is bound to the doublet microtubule and is connected to neighboring structures.
SourceChlamydomonas reinhardtii / plant / unicellular green algae
Map dataThis is a subtomogram average of the I1 inner dynein complex in wild type Chlamydomonas flagella
Methodsubtomogram averaging, at 39 A resolution
AuthorsHeuser T / Barber CF / Lin J / Krell J / Rebesco M / Porter ME / Nicastro D
CitationProc. Natl. Acad. Sci. U.S.A., 2012, 109, E2067-E2076

Proc. Natl. Acad. Sci. U.S.A., 2012, 109, E2067-E2076 StrPapers
Cryoelectron tomography reveals doublet-specific structures and unique interactions in the I1 dynein.
Thomas Heuser / Cynthia F Barber / Jianfeng Lin / Jeremy Krell / Matthew Rebesco / Mary E Porter / Daniela Nicastro

DateDeposition: Aug 10, 2011 / Header (metadata) release: Aug 11, 2011 / Map release: Jun 21, 2012 / Last update: Aug 10, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 127.5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 127.5
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_5330.map.gz (map file in CCP4 format, 345 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
40 pix
9.5 A/pix
= 380. A
40 pix
9.5 A/pix
= 522.5 A
55 pix
9.5 A/pix
= 380. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 9.5 A
Density
Contour Level:127.5 (by author), 127.5 (movie #1):
Minimum - Maximum109.59519958 - 148.88063049
Average (Standard dev.)124.20162964 (5.68234873)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions405540
Origin-53-21-64
Limit-1433-25
Spacing554040
CellA: 380 A / B: 522.5 A / C: 380 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z9.59.59.5
M x/y/z405540
origin x/y/z0.0000.0000.000
length x/y/z380.000522.500380.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-21-53-64
NC/NR/NS554040
D min/max/mean109.595148.881124.202

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Supplemental data

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Sample components

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Entire Cryo-electron tomography and subtomographic average (750 axonemal...

EntireName: Cryo-electron tomography and subtomographic average (750 axonemal repeats) of isolated axonemes of wild type Chlamydomonas (CC 125, 137c), I1 dynein complex (dynein f) is bound to the doublet microtubule and is connected to neighboring structures.
Number of components: 1

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Component #1: cellular-component, I1 dynein complex

Cellular-componentName: I1 dynein complex / a.k.a: dynein f / Recombinant expression: No / Number of Copies: 2
SourceSpecies: Chlamydomonas reinhardtii / plant / unicellular green algae
Strain: CC-125, 137c
Source (natural)Organelle: eukaryotic flagella / Cell: Chlamydomonas reinhardtii

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Experimental details

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Sample preparation

Sample solutionSpecimen conc.: 1 mg/ml
Buffer solution: 10 mM HEPES, pH 7.4, 25 mM NaCl, 4 mM MgSO4, 1 mM EGTA, 0.1 mM EDTA
pH: 7.4
Support filmQuantifoil holey carbon grids Cu 200 mesh R2/2
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 100 K / Method: front-side blotting for 2-3 seconds

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F30 / Date: Feb 20, 2004
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 100 e/A2 / Illumination mode: OTHER
LensMagnification: 13500 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 6000 - 8000 nm / Energy filter: GATAN postcolumn filter GIF / Energy window: 0-20 eV
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Tilt Angle: -60 - 60 deg. / Temperature: 80 K
CameraDetector: GENERIC GATAN (2k x 2k)

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Image processing

ProcessingMethod: subtomogram averaging
Details: 750 axonemal repeats (96 nm long) from 5 tomograms (reconstructed using fiducial alignment and weighted backprojection, IMOD software, Kremer et al. 1996) were aligned and averaged using the PEET software (bio3d.colorado.edu, Nicastro et al. 2006). Average number of tilts used in the 3D reconstructions: 80. Average tomographic tilt angle increment: 1.5.
3D reconstructionAlgorithm: fiducial alignment and weighted backprojection / Software: IMOD
Details: Final maps were calculated by averaging 750 particles from 5 tomograms
Resolution: 39 A / Resolution method: FSC 0.5

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