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- EMDB-1442: The role of the kinesin-13 neck in microtubule depolymerization. -

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Basic information

Entry
Database: EMDB / ID: EMD-1442
TitleThe role of the kinesin-13 neck in microtubule depolymerization.
Map dataA realspace map of kinesin-13-bound, 15 protofilament microtubules, calculated from averaged layer line data using Fourier-Bessel synthesis
Sample
  • Sample: Malarial kinesin-13 motor core ADPAlF
  • Protein or peptide: kinesin-13 motor core
  • Protein or peptide: tubulin
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Methodhelical reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsMoores CA / Hekmat-Nejad M / Sakowicz R / Milligan RA
CitationJournal: Cell Cycle / Year: 2006
Title: The role of the kinesin-13 neck in microtubule depolymerization.
Authors: Carolyn A Moores / Jeremy Cooper / Mike Wagenbach / Yulia Ovechkina / Linda Wordeman / Ronald A Milligan /
Abstract: To ensure genetic integrity, replicated chromosomes must be accurately distributed to daughter cells-a process that is accomplished on the microtubule spindle. Kinesin-13 motors play an essential ...To ensure genetic integrity, replicated chromosomes must be accurately distributed to daughter cells-a process that is accomplished on the microtubule spindle. Kinesin-13 motors play an essential role in this process by performing regulated microtubule depolymerization. We set out to dissect the depolymerization mechanism of these kinesins, and in particular, the role of their conserved neck sequence. We used a monomeric kinesin-13 MCAK, consisting of the neck and motor core, which has strong depolymerizing activity. In the presence of a non-hydrolysable ATP analogue, this construct induced formation of rings around microtubules. The rings are built from tubulin protofilaments that are bent by the kinesin-13 motor engaged at the ATP-binding step of its ATPase cycle. Our data suggest that the ring-microtubule interaction is mediated by the neck and support the idea of a role for the kinesin-13 neck in depolymerization efficiency, acting by optimizing release of tubulin from microtubule ends.
History
DepositionOct 8, 2007-
Header (metadata) releaseOct 8, 2007-
Map releaseOct 8, 2007-
UpdateFeb 20, 2013-
Current statusFeb 20, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 10
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 10
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1442.gif

Downloads & links

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Map

FileDownload / File: emd_1442.map.gz / Format: CCP4 / Size: 2.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA realspace map of kinesin-13-bound, 15 protofilament microtubules, calculated from averaged layer line data using Fourier-Bessel synthesis
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.97 Å/pix.
x 73 pix.
= 362.81 Å		4.97 Å/pix.
x 101 pix.
= 501.97 Å		4.97 Å/pix.
x 101 pix.
= 501.97 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 4.97 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 27.0 / Movie #1: 10
Minimum - Maximum-38.0 - 54.0
Average (Standard dev.)1.30652 (±10.3636)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10110173
Spacing10110173
CellA: 501.97 Å / B: 501.97 Å / C: 362.81 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
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-38.00054.0001.307

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Supplemental data

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Sample components

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Entire : Malarial kinesin-13 motor core ADPAlF

EntireName: Malarial kinesin-13 motor core ADPAlF
Components
  • Sample: Malarial kinesin-13 motor core ADPAlF
  • Protein or peptide: kinesin-13 motor core
  • Protein or peptide: tubulin

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Supramolecule #1000: Malarial kinesin-13 motor core ADPAlF

SupramoleculeName: Malarial kinesin-13 motor core ADPAlF / type: sample / ID: 1000 / Details: Molecular weight of kinesin motor core is 40kD
Oligomeric state: monomeric kinesin binds to each tubulin dimer
Number unique components: 2

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Macromolecule #1: kinesin-13 motor core

MacromoleculeName: kinesin-13 motor core / type: protein_or_peptide / ID: 1 / Name.synonym: pKinI / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
synonym: Malaria
Molecular weightExperimental: 40 KDa / Theoretical: 40 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #2: tubulin

MacromoleculeName: tubulin / type: protein_or_peptide / ID: 2 / Oligomeric state: helical polymer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
synonym: Malaria / Tissue: brain / Cell: neurone / Location in cell: cytoplasmic
Molecular weightExperimental: 100 KDa / Theoretical: 100 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration3 mg/mL
BufferpH: 6.8
Details: 2mM ADP, 8mM NaF, 2mM AlCl3, 20mM Pipes, 2mM MgCl2, 1mM EGTA, 1mM DTT
GridDetails: 400 mesh quantifoil grid 2/2
VitrificationCryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: plunger. vitrification performed in humidified cold room
Method: blot for 3-4s before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
TemperatureAverage: 95 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at
DateAug 1, 2002
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PERKIN ELMER / Digitization - Sampling interval: 20 µm / Number real images: 50 / Average electron dose: 10 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.95 µm / Nominal magnification: 38000
Sample stageSpecimen holder: side entry, nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Software - Name: Phoelix / Details: Final map calculated from 53 moire repeats
CTF correctionDetails: each microtubule

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