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- EMDB-8528: Cryo-EM structure of 8nm repeat tubulin lattice of the ciliary mi... -

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Basic information

Entry
Database: EMDB / ID: 8528
TitleCryo-EM structure of 8nm repeat tubulin lattice of the ciliary microtubule doublet
Map dataTubulin lattice of the microtubule doublet from Tetrahymena thermophila (8nm repeat)
Sample8nm-repeat tubulin lattice of microtubule doublet
  • Tubulin alpha chain
  • Tubulin beta chain
  • (ligand) x 3
Function/homologyBeta tubulin, autoregulation binding site / Tubulin-beta mRNA autoregulation signal. / Beta tubulin / Alpha tubulin / Tubulin / Tubulin, C-terminal / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / microtubule-based process / Tubulin/FtsZ, C-terminal domain superfamily ...Beta tubulin, autoregulation binding site / Tubulin-beta mRNA autoregulation signal. / Beta tubulin / Alpha tubulin / Tubulin / Tubulin, C-terminal / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / microtubule-based process / Tubulin/FtsZ, C-terminal domain superfamily / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / structural constituent of cytoskeleton / Tubulin C-terminal domain / Tubulin/FtsZ family, GTPase domain / microtubule / GTPase activity / GTP binding / cytoplasm / Tubulin alpha chain / Tubulin beta chain
Function and homology information
SourceTetrahymena thermophila / Tetrahymena / eukaryote
MethodCryo EM / single particle reconstruction / 5.7 Å resolution
AuthorsIchikawa M / Liu D
CitationJournal: Nat Commun / Year: 2017
Title: Subnanometre-resolution structure of the doublet microtubule reveals new classes of microtubule-associated proteins.
Authors: Muneyoshi Ichikawa / Dinan Liu / Panagiotis L Kastritis / Kaustuv Basu / Tzu Chin Hsu / Shunkai Yang / Khanh Huy Bui
Abstract: Cilia are ubiquitous, hair-like appendages found in eukaryotic cells that carry out functions of cell motility and sensory reception. Cilia contain an intriguing cytoskeletal structure, termed the ...Cilia are ubiquitous, hair-like appendages found in eukaryotic cells that carry out functions of cell motility and sensory reception. Cilia contain an intriguing cytoskeletal structure, termed the axoneme that consists of nine doublet microtubules radially interlinked and longitudinally organized in multiple specific repeat units. Little is known, however, about how the axoneme allows cilia to be both actively bendable and sturdy or how it is assembled. To answer these questions, we used cryo-electron microscopy to structurally analyse several of the repeating units of the doublet at sub-nanometre resolution. This structural detail enables us to unambiguously assign α- and β-tubulins in the doublet microtubule lattice. Our study demonstrates the existence of an inner sheath composed of different kinds of microtubule inner proteins inside the doublet that likely stabilizes the structure and facilitates the specific building of the B-tubule.
Validation ReportPDB-ID: 5ubq

SummaryFull reportAbout validation report
DateDeposition: Dec 21, 2016 / Header (metadata) release: Feb 8, 2017 / Map release: May 10, 2017 / Last update: Sep 27, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.105
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.105
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5ubq
  • Surface level: 0.105
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5ubq
  • Surface level: 0.105
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5ubq
  • Imaged by Jmol
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3D viewer
Supplemental images

Downloads & links

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Map

Fileemd_8528.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.75 Å
Density
Contour Level:0.105 (by author), 0.105 (movie #1):
Minimum - Maximum-0.16910973 - 0.38472342
Average (Standard dev.)0.0043363087 (0.03189638)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
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
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1690.3850.004

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Supplemental data

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Sample components

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Entire 8nm-repeat tubulin lattice of microtubule doublet

EntireName: 8nm-repeat tubulin lattice of microtubule doublet / Number of components: 6

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Component #1: cellular-component, 8nm-repeat tubulin lattice of microtubule doublet

Cellular-componentName: 8nm-repeat tubulin lattice of microtubule doublet / Recombinant expression: No
SourceSpecies: Tetrahymena thermophila / Strain: SB255
Source (natural)Organelle: cilia / Location in cell: cilia

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Component #2: protein, Tubulin alpha chain

ProteinName: Tubulin alpha chain / Recombinant expression: No
MassTheoretical: 48.788254 kDa
SourceSpecies: Tetrahymena thermophila

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Component #3: protein, Tubulin beta chain

ProteinName: Tubulin beta chain / Recombinant expression: No
MassTheoretical: 48.009199 kDa
SourceSpecies: Tetrahymena thermophila

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Component #4: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.52318 kDa
SourceSpecies:

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Component #5: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 2.430505 MDa
SourceSpecies:

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Component #6: ligand, GUANOSINE-5'-DIPHOSPHATE

LigandName: GUANOSINE-5'-DIPHOSPHATE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.443201 kDa
SourceSpecies:

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Experimental details

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Sample preparation

SpecimenSpecimen state: filament / Method: Cryo EM
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

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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
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 5983

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 127429
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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