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- EMDB-1441: The role of the kinesin-13 neck in microtubule depolymerization. -

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Basic information

Entry
Database: EMDB / ID: 1441
TitleThe role of the kinesin-13 neck in microtubule depolymerization.
SampleMalarial kinesin-13 motor core ADP
SourcePlasmodium falciparum / eukaryote / Malaria / マラリア病原虫, 熱帯熱マラリア原虫, 熱帯熱病原虫 /
Map dataA realspace map of kinesin-13-bound, 15 protofilament microtubules, calculated from averaged layer line data using Fourier-Bessel synthesis
Methodhelical reconstruction, at 20 A resolution
AuthorsMoores CA / Hekmat-Nejad M / Sakowicz R / Milligan RA
CitationCell Cycle, 2006, 5, 1812-1815

Cell Cycle, 2006, 5, 1812-1815 StrPapers
The role of the kinesin-13 neck in microtubule depolymerization.
Carolyn A Moores / Jeremy Cooper / Mike Wagenbach / Yulia Ovechkina / Linda Wordeman / Ronald A Milligan

DateDeposition: Oct 8, 2007 / Header (metadata) release: Oct 8, 2007 / Map release: Oct 8, 2007 / Last update: Oct 8, 2007

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 10
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 10
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_1441.map.gz (map file in CCP4 format, 2910 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
73 pix
4.97 A/pix
= 362.81 A
101 pix
4.97 A/pix
= 501.97 A
101 pix
4.97 A/pix
= 501.97 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.97 A
Density
Contour Level:28, 10 (movie #1):
Minimum - Maximum-37 - 48
Average (Standard dev.)1.62657 (10.558)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions10110173
Origin000
Limit10010072
Spacing10110173
CellA: 501.97 A / B: 501.97 A / C: 362.81 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z4.974.974.97
M x/y/z10110173
origin x/y/z0.0000.0000.000
length x/y/z501.970501.970362.810
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-60-60-59
NX/NY/NZ120120120
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS10110173
D min/max/mean-37.00048.0001.627

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Supplemental data

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Sample components

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Entire Malarial kinesin-13 motor core ADP

EntireName: Malarial kinesin-13 motor core ADP / Details: Molecular weight of kinesin motor core is 40kD
Oligomeric State: monomeric kinesin binds to each tubulin dimer
Number of components: 2

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Component #1: protein, kinesin-13 motor core

ProteinName: kinesin-13 motor core / a.k.a: pKinI / Oligomeric Details: monomer / Recombinant expression: Yes
MassTheoretical: 40 kDa / Experimental: 40 kDa
SourceSpecies: Plasmodium falciparum / eukaryote / Malaria / マラリア病原虫, 熱帯熱マラリア原虫, 熱帯熱病原虫 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: protein, tubulin

ProteinName: tubulin / Oligomeric Details: helical polymer / Recombinant expression: No
MassTheoretical: 100 kDa / Experimental: 100 kDa
SourceSpecies: Plasmodium falciparum / eukaryote / Malaria / マラリア病原虫, 熱帯熱マラリア原虫, 熱帯熱病原虫 /
Source (natural)Location in cell: cytoplasmic / Cell: neurone / Organ or tissue: brain

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Experimental details

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Sample preparation

Specimen statefilament
Helical parametersHand: LEFT HANDED
Sample solutionSpecimen conc.: 3 mg/ml
Buffer solution: 20mM Pipes, 2mM MgCl2, 1mM EGTA, 1mM DTT,5mM ADP
pH: 6.8
Support film400 mesh quantifoil grid 2/2
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 98 % / Method: blot for 3-4s before plunging
Details: Vitrification instrument: plunger. vitrification performed in humidified cold room

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG / Date: Aug 1, 2002
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 10 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 38000 X (nominal) / Astigmatism: objective lens astigmatism was corrected at / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 950 - 2200 nm
Specimen HolderHolder: side entry, nitrogen cooled / Model: GATAN LIQUID NITROGEN / Temperature: 95 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 50 / Scanner: PERKIN ELMER / Sampling size: 20 microns

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: Fourier Bessel synthesis / Software: Phoelix / CTF correction: each microtubule / Resolution: 20 A / Resolution method: layer line phase information / Details: Final map calculated from 184 moire repeats

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