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- EMDB-5027: Kinesin13-Microtubule Ring Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-5027
TitleKinesin13-Microtubule Ring Complex
Map dataKinesin 13-Microtubule Ring Complex
Sample
  • Sample: Kinesin13-Microtubule Ring Complex
  • Protein or peptide: KLP10a
  • Protein or peptide: alpha-tubulin
  • Protein or peptide: beta-tubulin
KeywordsKinesin / Kinesin-13 / microtubule / tubulin / depolymerization / Kin-I / M-Kinesin / cytoskeleton
Function / homology
Function and homology information


postsynaptic cytoskeleton organization / regulation of chromosome segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / establishment or maintenance of microtubule cytoskeleton polarity / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / metaphase chromosome alignment / Resolution of Sister Chromatid Cohesion / COPI-dependent Golgi-to-ER retrograde traffic ...postsynaptic cytoskeleton organization / regulation of chromosome segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / establishment or maintenance of microtubule cytoskeleton polarity / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / metaphase chromosome alignment / Resolution of Sister Chromatid Cohesion / COPI-dependent Golgi-to-ER retrograde traffic / RHO GTPases Activate Formins / Separation of Sister Chromatids / microtubule plus-end / attachment of mitotic spindle microtubules to kinetochore / MHC class II antigen presentation / microtubule plus-end binding / microtubule depolymerization / microtubule motor activity / motile cilium / tubulin complex / microtubule-based movement / mitotic metaphase chromosome alignment / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / chromosome, centromeric region / kinetochore / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / mitotic cell cycle / presynapse / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / postsynapse / hydrolase activity / cell division / GTPase activity / GTP binding / glutamatergic synapse / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / Kinesin-like protein KIF2A-like, N-terminal / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily ...: / Kinesin-like protein KIF2A-like, N-terminal / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / Alpha tubulin / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Tubulin alpha-1A chain / Tubulin beta chain / Tubulin alpha-1D chain / Kinesin-like protein KIF2C
Similarity search - Component
Methodhelical reconstruction / cryo EM / Resolution: 28.0 Å
AuthorsTan D / Rice WJ / Sosa H
CitationJournal: Structure / Year: 2008
Title: Structure of the kinesin13-microtubule ring complex.
Authors: Dongyan Tan / William J Rice / Hernando Sosa /
Abstract: To investigate the mechanism of kinesin13-induced microtubule depolymerization, we have calculated a three-dimensional (3D) map of the kinesin13-microtubule ring complex, using cryo-electron ...To investigate the mechanism of kinesin13-induced microtubule depolymerization, we have calculated a three-dimensional (3D) map of the kinesin13-microtubule ring complex, using cryo-electron microscopy (cryo-EM) and image analysis. An atomic model of the complex was produced by docking the crystal structures of tubulin and a kinesin13 motor domain (MD) into the 3D map. The model reveals a snapshot of the depolymerization mechanism by providing a 3D view of the complex formed between the kinesin13 MD and a curved tubulin protofilament (pf). It suggests that contacts mediated by kinesin13 class-specific residues in the putative microtubule-binding site stabilize intra-dimer tubulin curvature. In addition, a tubulin-binding site on the kinesin13 MD was identified. Mutations at this class-conserved site selectively disrupt the formation of microtubule-associated ring complexes.
History
DepositionAug 29, 2008-
Header (metadata) releaseDec 17, 2008-
Map releaseMay 5, 2009-
UpdateApr 2, 2014-
Current statusApr 2, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 14
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 14
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3edl
  • Surface level: 14
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3edl
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5027_1.tif

Downloads & links

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Map

FileDownload / File: emd_5027.map.gz / Format: CCP4 / Size: 1.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationKinesin 13-Microtubule Ring Complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6 Å/pix.
x 41 pix.
= 246. Å		6 Å/pix.
x 101 pix.
= 606. Å		6 Å/pix.
x 101 pix.
= 606. 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: 6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 11.1 / Movie #1: 14
Minimum - Maximum-48.0 - 55.0
Average (Standard dev.)0.56261343 (±12.836534500000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10110141
Spacing10110141
CellA: 606.0 Å / B: 606.0 Å / C: 246.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z666
M x/y/z10110141
origin x/y/z0.0000.0000.000
length x/y/z606.000606.000246.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-127-127-127
NX/NY/NZ255255255
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS10110141
D min/max/mean-48.00055.0000.563

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Supplemental data

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Sample components

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Entire : Kinesin13-Microtubule Ring Complex

EntireName: Kinesin13-Microtubule Ring Complex
Components
  • Sample: Kinesin13-Microtubule Ring Complex
  • Protein or peptide: KLP10a
  • Protein or peptide: alpha-tubulin
  • Protein or peptide: beta-tubulin

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Supramolecule #1000: Kinesin13-Microtubule Ring Complex

SupramoleculeName: Kinesin13-Microtubule Ring Complex / type: sample / ID: 1000 / Number unique components: 3
Molecular weightExperimental: 250 KDa / Theoretical: 250 KDa / Method: SDS-PAGE

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Macromolecule #1: KLP10a

MacromoleculeName: KLP10a / type: protein_or_peptide / ID: 1 / Name.synonym: Kinesin-13 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Cell: BL21 / Location in cell: cytosol
Molecular weightExperimental: 400 KDa / Theoretical: 400 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pRSET B

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Macromolecule #2: alpha-tubulin

MacromoleculeName: alpha-tubulin / type: protein_or_peptide / ID: 2 / Name.synonym: tubulin / Number of copies: 2 / Oligomeric state: Heterodimer / Recombinant expression: No / Database: NCBI
Source (natural)Tissue: Bos taurus Brain
Molecular weightExperimental: 550 KDa
SequenceGO: tubulin complex / InterPro: Alpha tubulin

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Macromolecule #3: beta-tubulin

MacromoleculeName: beta-tubulin / type: protein_or_peptide / ID: 3 / Name.synonym: tubulin / Number of copies: 2 / Oligomeric state: Hterodimer / Recombinant expression: No / Database: NCBI
Source (natural)Tissue: Brain
Molecular weightExperimental: 550 KDa
SequenceGO: tubulin complex / InterPro: Beta tubulin

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.6 mg/mL
BufferpH: 6.8
Details: 80 mM Pipes, pH 6.8, 2 mM MgCl2, 1 mM EGTA, 2 mM AMP-PNP, 0.02 mM taxol
GridDetails: Quantifoil grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: VitroBot
Method: Blot for 2 seconds, Blot Offset (mm) -2, Plunge Time 1 sec, Wait Time 0 sec

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI TECNAI 20
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 12.5 µm / Number real images: 5 / Average electron dose: 9 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN

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Electron microscopy #2

Microscopy ID2
MicroscopeFEI TECNAI F20
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 12.5 µm / Number real images: 5 / Average electron dose: 9 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: MRC, SUPRIM, Phoelix, Other
Details: Final map is the averaged near and far layer line data from 5 filaments (10 datasets, 3296 asymmetric units)
CTF correctionDetails: Each Particle

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Atomic model buiding 1

Initial modelPDB ID:

1v8k


Chain - Chain ID: A
SoftwareName: COLORES
DetailsPDBEntryID_givenInChain. Protocol: Rigid-Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3edl:
Kinesin13-Microtubule Ring complex

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Atomic model buiding 2

Initial modelPDB ID:

1jff

SoftwareName: COLORES
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3edl:
Kinesin13-Microtubule Ring complex

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Atomic model buiding 3

Initial modelPDB ID:

1sa0

SoftwareName: COLORES
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3edl:
Kinesin13-Microtubule Ring complex

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