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- EMDB-8408: Cryo-EM reconstruction of the yeast kinesin-5, Cin8, bound to GDP... -

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Basic information

Entry
Database: EMDB / ID: 8408
TitleCryo-EM reconstruction of the yeast kinesin-5, Cin8, bound to GDP-taxol microtubules in ADP-AlFx state
SampleMicrotubule-bound kinesin-5 Cin8 in ADP-AlFx state
SourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Map data3D helical reconstruction of Cin8 motor domain in ADP-AlFx state bound to microtubule using cryo-EM
Methodhelical reconstruction, at 7.3 Å resolution
AuthorsCha HK
CitationJ. Biol. Chem., 2017, 292, 14680-14694

J. Biol. Chem., 2017, 292, 14680-14694 Yorodumi Papers
The yeast kinesin-5 Cin8 interacts with the microtubule in a noncanonical manner.
Kayla M Bell / Hyo Keun Cha / Charles V Sindelar / Jared C Cochran

DateDeposition: Oct 1, 2016 / Header (metadata) release: Oct 12, 2016 / Map release: Jul 26, 2017 / Last update: Sep 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0957
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0957
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0957
  • Imaged by UCSF CHIMERA
  • Download
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Map

Fileemd_8408.map.gz (map file in CCP4 format, 87809 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
280 pix
2.49 Å/pix.
= 698.326 Å
280 pix
2.49 Å/pix.
= 698.326 Å
280 pix
2.49 Å/pix.
= 698.326 Å

Surface

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Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.49402 Å
Density
Contour Level:0.0957 (by author), 0.0957 (movie #1):
Minimum - Maximum0 - 0.21301804
Average (Standard dev.)0.0074020033 (0.024142148)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions280280280
Origin-140-140-140
Limit139139139
Spacing280280280
CellA=B=C: 698.3256 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.49402142857142.49402142857142.4940214285714
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z698.326698.326698.326
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-140-140-140
NC/NR/NS280280280
D min/max/mean0.0000.2130.007

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Supplemental data

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Sample components

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Entire Microtubule-bound kinesin-5 Cin8 in ADP-AlFx state

EntireName: Microtubule-bound kinesin-5 Cin8 in ADP-AlFx state
Details: Cin8-his monomer (residues 70-535) Taxol-stabilized microtubules
Number of components: 1

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Component #1: protein, Microtubule-bound kinesin-5 Cin8 in ADP-AlFx state

ProteinName: Microtubule-bound kinesin-5 Cin8 in ADP-AlFx state
Details: Cin8-his monomer (residues 70-535) Taxol-stabilized microtubules
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pET16b / Cell of expression system: B834(DE3)

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Experimental details

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Sample preparation

Specimen statefilament
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 9.455 Å / Delta phi: -25.77 deg.
Sample solutionBuffer solution: adjusted to pH 6.8 with KOH / pH: 6.8
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1.71 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: FREALIGN / Resolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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External links: The 2017 Nobel Prize in Chemistry - Press Release

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