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- EMDB-5565: CS-tubulin Kinesin-13 Microtubule complex -

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Basic information

Entry
Database: EMDB / ID: EMD-5565
TitleCS-tubulin Kinesin-13 Microtubule complex
Map dataReconstruction of the kinesin-13 KLP10A head domain in complex with CS-tubulin and a microtubule
Sample
  • Sample: kinesin-13 KLP10A head domain in complex with CS-tubulin and a microtubule
  • Protein or peptide: KLP10A
  • Protein or peptide: Tubulin alpha-1A chain
  • Protein or peptide: Tubulin beta-2B chain
Keywordstubulin / microtubule / depolymerase / depolymerization / kinI / kinesin-13 / kinesin
Function / homology
Function and homology information


establishment of mitotic spindle asymmetry / establishment of meiotic spindle orientation / cortical microtubule / plus-end specific microtubule depolymerization / asymmetric protein localization involved in cell fate determination / meiotic spindle pole / mitotic spindle astral microtubule / centriole assembly / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins ...establishment of mitotic spindle asymmetry / establishment of meiotic spindle orientation / cortical microtubule / plus-end specific microtubule depolymerization / asymmetric protein localization involved in cell fate determination / meiotic spindle pole / mitotic spindle astral microtubule / centriole assembly / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / mitotic chromosome movement towards spindle pole / kinetochore microtubule / meiotic spindle organization / spindle assembly involved in female meiosis I / non-motile cilium assembly / plus-end-directed microtubule motor activity / meiotic spindle / positive regulation of axon guidance / microtubule depolymerization / kinesin complex / microtubule motor activity / spindle organization / microtubule-based movement / mitotic spindle pole / cytoskeletal motor activity / centrosome duplication / chromosome, centromeric region / cytoplasmic microtubule / microtubule-based process / cellular response to interleukin-4 / mitotic spindle organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / spindle / microtubule cytoskeleton organization / spindle pole / microtubule cytoskeleton / double-stranded RNA binding / mitotic cell cycle / nervous system development / microtubule binding / microtubule / protein heterodimerization activity / cell division / GTPase activity / centrosome / ubiquitin protein ligase binding / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
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 / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin ...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 / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / 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-1B chain / Tubulin beta-2B chain / Kinesin-like protein Klp10A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly) / Bos taurus (cattle)
Methodhelical reconstruction / cryo EM / Resolution: 10.8 Å
AuthorsAsenjo AB / Chatterjee C / Tan D / DePaoli V / Rice WJ / Diaz-Avalos R / Silvestry M / Sosa H
CitationJournal: Cell Rep / Year: 2013
Title: Structural model for tubulin recognition and deformation by kinesin-13 microtubule depolymerases.
Authors: Ana B Asenjo / Chandrima Chatterjee / Dongyan Tan / Vania DePaoli / William J Rice / Ruben Diaz-Avalos / Mariena Silvestry / Hernando Sosa /
Abstract: To elucidate the structural basis of the mechanism of microtubule depolymerization by kinesin-13s, we analyzed complexes of tubulin and the Drosophila melanogaster kinesin-13 KLP10A by electron ...To elucidate the structural basis of the mechanism of microtubule depolymerization by kinesin-13s, we analyzed complexes of tubulin and the Drosophila melanogaster kinesin-13 KLP10A by electron microscopy (EM) and fluorescence polarization microscopy. We report a nanometer-resolution (1.1 nm) cryo-EM three-dimensional structure of the KLP10A head domain (KLP10AHD) bound to curved tubulin. We found that binding of KLP10AHD induces a distinct tubulin configuration with displacement (shear) between tubulin subunits in addition to curvature. In this configuration, the kinesin-binding site differs from that in straight tubulin, providing an explanation for the distinct interaction modes of kinesin-13s with the microtubule lattice or its ends. The KLP10AHD-tubulin interface comprises three areas of interaction, suggesting a crossbow-type tubulin-bending mechanism. These areas include the kinesin-13 family conserved KVD residues, and as predicted from the crossbow model, mutating these residues changes the orientation and mobility of KLP10AHDs interacting with the microtubule.
History
DepositionJan 9, 2013-
Header (metadata) releaseFeb 20, 2013-
Map releaseMar 6, 2013-
UpdateApr 10, 2013-
Current statusApr 10, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j2u
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j2u
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5565.map.gz / Format: CCP4 / Size: 25.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the kinesin-13 KLP10A head domain in complex with CS-tubulin and a microtubule
Voxel sizeX=Y=Z: 2 Å
Density
Contour LevelBy EMDB: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.12360548 - 0.15922026
Average (Standard dev.)0.00000776 (±0.02484056)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions29029080
Spacing29029080
CellA: 580.0 Å / B: 580.0 Å / C: 160.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z29029080
origin x/y/z0.0000.0000.000
length x/y/z580.000580.000160.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS29029080
D min/max/mean-0.1240.1590.000

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Supplemental data

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Sample components

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Entire : kinesin-13 KLP10A head domain in complex with CS-tubulin and a mi...

EntireName: kinesin-13 KLP10A head domain in complex with CS-tubulin and a microtubule
Components
  • Sample: kinesin-13 KLP10A head domain in complex with CS-tubulin and a microtubule
  • Protein or peptide: KLP10A
  • Protein or peptide: Tubulin alpha-1A chain
  • Protein or peptide: Tubulin beta-2B chain

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Supramolecule #1000: kinesin-13 KLP10A head domain in complex with CS-tubulin and a mi...

SupramoleculeName: kinesin-13 KLP10A head domain in complex with CS-tubulin and a microtubule
type: sample / ID: 1000 / Oligomeric state: Helical / Number unique components: 2

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Macromolecule #1: KLP10A

MacromoleculeName: KLP10A / type: protein_or_peptide / ID: 1 / Name.synonym: kinesin-13, kinI / Details: KLP10A head domain / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit fly / Location in cell: cytoplasm
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Kinesin-like protein Klp10A

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Macromolecule #2: Tubulin alpha-1A chain

MacromoleculeName: Tubulin alpha-1A chain / type: protein_or_peptide / ID: 2 / Details: Dimer with Tubulin beta-2B chain / Oligomeric state: helical multimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (cattle) / synonym: bovine / Tissue: brain
SequenceUniProtKB: Tubulin alpha-1B chain

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Macromolecule #3: Tubulin beta-2B chain

MacromoleculeName: Tubulin beta-2B chain / type: protein_or_peptide / ID: 3 / Details: Dimer with Tubulin alpha-1A chain / Oligomeric state: helical multimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (cattle) / synonym: bovine / Tissue: brain
SequenceUniProtKB: Tubulin beta-2B chain

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK I

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Electron microscopy #1

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: JEOL
Microscopy ID1
DateMay 1, 2012
Image recordingDigitization - Scanner: OTHER

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Electron microscopy #2

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder: Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN
Microscopy ID2
DateMay 1, 2012
Image recordingDigitization - Scanner: OTHER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Helical parameters - Δz: 5.55267 Å
Applied symmetry - Helical parameters - Δ&Phi: 168.08743 °
Resolution.type: BY AUTHOR / Resolution: 10.8 Å / Resolution method: OTHER / Software - Name: Spider, IHRSR, CTFFIND3, Custom
DetailsCustom single particle alignment method based on IHRSR

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