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- EMDB-9385: The central pair complex of sea urchin (Strongylocentrotus purpur... -

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Entry
Database: EMDB / ID: 9385
TitleThe central pair complex of sea urchin (Strongylocentrotus purpuratus) sperm resolved by cryo-electron tomography and sub-tomogram averaging
Map dataThe central pair complex of sea urchin (Strongylocentrotus purpuratus) sperm resolved by cryo-electron tomography and sub-tomogram averaging
SampleThe central pair complex/apparatus (2167 repeats) averaged from 41 Strongylocentrotus sea urchin sperms:
SourceStrongylocentrotus purpuratus (purple sea urchin)
Methodsubtomogram averaging / cryo EM / 35 Å resolution
AuthorsCarbajal-Gonzalez BI / Heuser T / Fu X / Lin J / Smith BW / Mitchell DR / Fu G / Nicastro D
CitationJournal: Cytoskeleton (Hoboken) / Year: 2013
Title: Conserved structural motifs in the central pair complex of eukaryotic flagella.
Authors: Blanca I Carbajal-González / Thomas Heuser / Xiaofeng Fu / Jianfeng Lin / Brandon W Smith / David R Mitchell / Daniela Nicastro
Abstract: Cilia and flagella are conserved hair-like appendages of eukaryotic cells that function as sensing and motility generating organelles. Motility is driven by thousands of axonemal dyneins that require ...Cilia and flagella are conserved hair-like appendages of eukaryotic cells that function as sensing and motility generating organelles. Motility is driven by thousands of axonemal dyneins that require precise regulation. One essential motility regulator is the central pair complex (CPC) and many CPC defects cause paralysis of cilia/flagella. Several human diseases, such as immotile cilia syndrome, show CPC abnormalities, but little is known about the detailed three-dimensional (3D) structure and function of the CPC. The CPC is located in the center of typical [9+2] cilia/flagella and is composed of two singlet microtubules (MTs), each with a set of associated projections that extend toward the surrounding nine doublet MTs. Using cryo-electron tomography coupled with subtomogram averaging, we visualized and compared the 3D structures of the CPC in both the green alga Chlamydomonas and the sea urchin Strongylocentrotus at the highest resolution published to date. Despite the evolutionary distance between these species, their CPCs exhibit remarkable structural conservation. We identified several new projections, including those that form the elusive sheath, and show that the bridge has a more complex architecture than previously thought. Organism-specific differences include the presence of MT inner proteins in Chlamydomonas, but not Strongylocentrotus, and different overall outlines of the highly connected projection network, which forms a round-shaped cylinder in algae, but is more oval in sea urchin. These differences could be adaptations to the mechanical requirements of the rotating CPC in Chlamydomonas, compared to the Strongylocentrotus CPC which has a fixed orientation.
DateDeposition: Jan 2, 2019 / Header (metadata) release: Jan 16, 2019 / Map release: Jan 16, 2019 / Last update: Jan 16, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 126
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 126
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9385.map.gz (map file in CCP4 format, 4001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
9.86 Å/pix.
= 985.6 Å
100 pix
9.86 Å/pix.
= 985.6 Å
100 pix
9.86 Å/pix.
= 985.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 9.856 Å
Density
Contour Level:126.0 (by author), 126 (movie #1):
Minimum - Maximum107.892334000000005 - 139.692520000000002
Average (Standard dev.)118.929749999999999 (4.037084)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin0.00.00.0
Limit99.099.099.0
Spacing100100100
CellA=B=C: 985.6 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z9.8569.8569.856
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z985.600985.600985.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean107.892139.693118.930

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Supplemental data

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Sample components

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Entire The central pair complex/apparatus (2167 repeats) averaged from 4...

EntireName: The central pair complex/apparatus (2167 repeats) averaged from 41 Strongylocentrotus sea urchin sperms
Number of components: 1

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Component #1: cellular-component, The central pair complex/apparatus (2167 repe...

Cellular-componentName: The central pair complex/apparatus (2167 repeats) averaged from 41 Strongylocentrotus sea urchin sperms
Recombinant expression: No
SourceSpecies: Strongylocentrotus purpuratus (purple sea urchin)
Source (natural)Organelle: sperm / Location in cell: tail of sperm

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Experimental details

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Sample preparation

SpecimenSpecimen state: cell / Method: cryo EM
Sample solutionBuffer solution: artificial sea water / pH: 7.4
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 298 K
Details: back-side blotting for 1.5-2.5 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 13500.0 X (calibrated) / Imaging mode: BRIGHT FIELD / Energy filter: GIF 2000
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN ULTRASCAN 1000 (2k x 2k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 2167
3D reconstructionAlgorithm: BACK PROJECTION / Software: IMOD / Resolution: 35 Å / Resolution method: FSC 0.5 CUT-OFF

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