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- EMDB-1701: The molecular mechanism of the multi-tasking kinesin-8 motor -

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Entry
Database: EMDB / ID: 1701
TitleThe molecular mechanism of the multi-tasking kinesin-8 motor
KeywordsMolecular motor / kinesin 8 / ruby-helix
SampleMicrotubule complexed with motor domain of Kif18A (no nucleotide state)
SourceHomo sapiens / human
Bos taurus / mammal / ウシ /
Map data10A reconstruction of a 15pf microtubule decorated with the motor domain of Kif18A (kinesin 8) in the Apo-state
Methodhelical reconstruction, at 10.1 Å resolution
AuthorsPeters C / Brejc K / Belmont L / Bodey A / Lee Y / Yu M / Ramchandani S / Guo J / Lichtsteiner S / Wood KW / Sakowicz R / Hartman J / Moores C
CitationEMBO J., 2010, 29, 3437-3447

EMBO J., 2010, 29, 3437-3447 Yorodumi Papers
Insight into the molecular mechanism of the multitasking kinesin-8 motor.
Carsten Peters / Katjuša Brejc / Lisa Belmont / Andrew J Bodey / Yan Lee / Ming Yu / Jun Guo / Roman Sakowicz / James Hartman / Carolyn A Moores

DateDeposition: Feb 9, 2010 / Header (metadata) release: Mar 10, 2010 / Map release: Oct 1, 2010 / Last update: Sep 9, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_1701.map.gz (map file in CCP4 format, 128001 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.4 Å/pix.
= 448. Å
320 pix
1.4 Å/pix.
= 448. Å
320 pix
1.4 Å/pix.
= 448. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.4 Å
Density
Contour Level:1 (by author), 1 (movie #1):
Minimum - Maximum-6.53806 - 8.76477
Average (Standard dev.)6.75811e-09 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin-159-160-160
Limit160159159
Spacing320320320
CellA=B=C: 448 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z448.000448.000448.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ121121121
MAP C/R/S123
start NC/NR/NS-160-159-160
NC/NR/NS320320320
D min/max/mean-6.5388.7650.000

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Supplemental data

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Sample components

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Entire Microtubule complexed with motor domain of Kif18A (no nucleotide ...

EntireName: Microtubule complexed with motor domain of Kif18A (no nucleotide state)
Number of components: 3

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Component #1: protein, Motor domain of Kif18A

ProteinName: Motor domain of Kif18A / a.k.a: Motor domain of Kif18A / Details: Contains the N-terminal 355 aa / Recombinant expression: Yes
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli rosetta de3 / bacteria / image: Escherichia coli
Source (natural)Location in cell: Cytoplasm

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Component #2: protein, Alpha tubulin

ProteinName: Alpha tubulin / a.k.a: Alpha tubulin / Recombinant expression: No
SourceSpecies: Bos taurus / mammal / ウシ /
Source (natural)Location in cell: Cytoplasm / Organ or tissue: brain

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Component #3: protein, Beta tubulin

ProteinName: Beta tubulin / a.k.a: Beta tubulin / Recombinant expression: No
SourceSpecies: Bos taurus / mammal / ウシ /
Source (natural)Location in cell: Cytoplasm / Organ or tissue: Brain

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Experimental details

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Sample preparation

Specimen statefilament
Helical parametersHand: RIGHT HANDED
Sample solutionBuffer solution: 80mM PIPES, 150mM NaCl, 7mM MgCl2, 1mM EGTA, 1mM beta-mercaptoethanol
pH: 6.8
Support film400 mesh copper grid
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Method: Blotted for 1 sec before plunging
Time resolved state: Vitrified after incubating with Apyrase
Details: Vitrification instrument: Manual plunger

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Details: Low dose
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 50000 X (calibrated)
Astigmatism: Objective lense stigmatism was corrected at 150,000 times magnification
Cs: 2 mm / Imaging mode: OTHER / Defocus: 920 - 3300 nm
Specimen HolderHolder: cryo-holder / Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 50 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 12

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: Helical processing / Software: Ruby-Helix / CTF correction: Phase flipping, Wiener
Details: Fourier Bessel Synthesis using data from 25 microtubules (36000 asymmetric units)
Resolution: 10.1 Å / Resolution method: FSC 0.5

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