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- EMDB-8532: Cryo-EM structure of 16nm repeat ciliary microtubule doublet -

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Basic information

Entry
Database: EMDB / ID: 8532
TitleCryo-EM structure of 16nm repeat ciliary microtubule doublet
Map data16nm repeat map of the doublet from Tetrahymena thermophila
Sample16nm-repeat of microtubule doublet
Function/homologyMalF, N-terminal / Maltose transport system permease protein MalF, P2 domain / Maltose transport system, permease protein MalF / ABC transporter, maltose/maltodextrin import, MalK / Maltose/Maltodextrin import ATP-binding protein malK family profile. / maltose transport complex / maltose-transporting ATPase / maltose-transporting ATPase activity / Transport-associated OB, type 2 / Maltose transport system permease protein MalF P2 domain ...MalF, N-terminal / Maltose transport system permease protein MalF, P2 domain / Maltose transport system, permease protein MalF / ABC transporter, maltose/maltodextrin import, MalK / Maltose/Maltodextrin import ATP-binding protein malK family profile. / maltose transport complex / maltose-transporting ATPase / maltose-transporting ATPase activity / Transport-associated OB, type 2 / Maltose transport system permease protein MalF P2 domain / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / ABC transporter integral membrane type-1 domain profile. / TOBE domain / Molybdate/tungstate binding, C-terminal / Binding-protein-dependent transport system inner membrane component / maltose transport / maltodextrin transport / ABC transporters family signature. / ABC transporter, conserved site / activating transcription factor binding / ABC transporter-like / ATP-binding cassette, ABC transporter-type domain profile. / ATP-binding cassette (ABC) transporter complex / ABC transporter / extrinsic component of cytoplasmic side of plasma membrane / AAA+ ATPase domain / cellular response to DNA damage stimulus / integral component of plasma membrane / P-loop containing nucleoside triphosphate hydrolase / membrane / ATP binding / plasma membrane / Maltose transport system permease protein MalF / Maltose transport system permease protein MalG / Maltose/maltodextrin import ATP-binding protein MalK
Function and homology information
SourceTetrahymena thermophila / eukaryote / Tetrahymena
Methodsingle particle reconstruction, at 6.2 Å resolution
AuthorsIchikawa M / Liu D / Kastritis PL / Basu K / Bui KH
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.
DateDeposition: Dec 21, 2016 / Header (metadata) release: Jan 18, 2017 / Map release: May 10, 2017 / Last update: Feb 14, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
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3D viewer
Supplemental images

Downloads & links

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Map

Fileemd_8532.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:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.074407496 - 0.15960655
Average (Standard dev.)0.0019532945 (0.014449678)
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/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0740.1600.002

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Supplemental data

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Sample components

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Entire 16nm-repeat of microtubule doublet

EntireName: 16nm-repeat of microtubule doublet / Number of components: 1

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Component #1: cellular-component, 16nm-repeat of microtubule doublet

Cellular-componentName: 16nm-repeat of microtubule doublet / Recombinant expression: No
SourceSpecies: Tetrahymena thermophila / eukaryote / Tetrahymena / Strain: SB255
Source (natural)Organelle: cilia / Location in cell: cilia

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Experimental details

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Sample preparation

Specimen statefilament
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 / Number of projections: 64116
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF

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