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- EMDB-8539: Cryo-EM map of protofilament of microtubule doublet -

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Basic information

Entry
Database: EMDB / ID: 8539
TitleCryo-EM map of protofilament of microtubule doublet
Map data
SampleProtofilament from ciliary microtubule doublet
Function/homologyTubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / 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-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / 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, 2-layer sandwich domain / Tubulin/FtsZ, C-terminal / 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 / Tubulin beta chain
Function and homology information
SourceTetrahymena thermophila / eukaryote / Tetrahymena
Methodsingle particle reconstruction, at 4.6 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: 5ucy

SummaryFull reportAbout validation report
DateDeposition: Dec 22, 2016 / Header (metadata) release: Feb 15, 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: 0.06
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.06
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5ucy
  • Surface level: 0.06
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5ucy
  • Imaged by Jmol
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3D viewer
Supplemental images

emd_8539.png

Downloads & links

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Map

Fileemd_8539.map.gz (map file in CCP4 format, 29206 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
194 pix
1.38 Å/pix.
= 266.75 Å		194 pix
1.38 Å/pix.
= 266.75 Å		194 pix
1.38 Å/pix.
= 266.75 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.375 Å
Density

Histogram

Histogram (log scale)
Contour Level:0.06 (by author), 0.06 (movie #1):
Minimum - Maximum-0.03319637 - 0.14551778
Average (Standard dev.)0.0012695125 (0.008444522)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions194194194
Origin000
Limit193193193
Spacing194194194
CellA=B=C: 266.75 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3751.3751.375
M x/y/z194194194
origin x/y/z0.0000.0000.000
length x/y/z266.750266.750266.750
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS194194194
D min/max/mean-0.0330.1460.001

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Supplemental data

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Sample components

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Entire Protofilament from ciliary microtubule doublet

EntireName: Protofilament from ciliary microtubule doublet / Number of components: 6

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Component #1: cellular-component, Protofilament from ciliary microtubule doublet

Cellular-componentName: Protofilament from ciliary microtubule doublet / Recombinant expression: No
SourceSpecies: Tetrahymena thermophila / eukaryote / Tetrahymena / Strain: SB255

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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 / Tetrahymena

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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 / Tetrahymena

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

LigandName: GUANOSINE-5'-TRIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

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Component #5: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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

LigandName: GUANOSINE-5'-DIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.443201 kDa

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Experimental details

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Sample preparation

Specimen statefilament
Sample solutionpH: 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: 23
3D reconstructionSoftware: Tom AV3 / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF
Details: 23 boxes of the protofilament are boxed out from the doublet map (EMD-8528), aligned and averaged using subtomogram averaging software.
Euler angles: Alignment using Tom AV3 software

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Atomic model buiding

Output model

5ucy

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