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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
SampleProtofilament from ciliary microtubule doublet
SourceTetrahymena thermophila / eukaryote
Map data
Methodsingle particle reconstruction, at 4.6 Å resolution
AuthorsIchikawa M / Liu D
CitationNat Commun, 2017, 8, 15035-15035

Nat Commun, 2017, 8, 15035-15035 StrPapers
Subnanometre-resolution structure of the doublet microtubule reveals new classes of microtubule-associated proteins.
Muneyoshi Ichikawa / Dinan Liu / Panagiotis L Kastritis / Kaustuv Basu / Tzu Chin Hsu / Shunkai Yang / Khanh Huy Bui

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: May 17, 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
3D viewer


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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
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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 / 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

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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'-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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