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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 C-terminal domain / Tubulin/FtsZ, C-terminal domain superfamily / Tubulin/FtsZ, GTPase domain superfamily / Tubulin, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin, conserved site / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, GTPase domain / Beta tubulin ...Beta tubulin, autoregulation binding site / Tubulin C-terminal domain / Tubulin/FtsZ, C-terminal domain superfamily / Tubulin/FtsZ, GTPase domain superfamily / Tubulin, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin, conserved site / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, GTPase domain / Beta tubulin / Alpha tubulin / Tubulin / Tubulin subunits alpha, beta, and gamma signature. / Tubulin-beta mRNA autoregulation signal. / Tubulin/FtsZ family, GTPase domain / microtubule-based process / structural constituent of cytoskeleton / microtubule / GTPase activity / GTP binding / cytoplasm / Tubulin alpha chain / Tubulin beta chain
Function and homology information
SourceTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / 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
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: May 16, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.105
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.105
  • Imaged by UCSF Chimera
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  • 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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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
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.

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: 704.0 Å
α=β=γ: 90.0 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 (eukaryote) / 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 (eukaryote)

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Component #3: protein, Tubulin beta chain

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

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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

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Component #5: ligand, MAGNESIUM ION

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

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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

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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: 1 % / 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: 1200.0 - 3800.0 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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