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- PDB-3j2u: Kinesin-13 KLP10A HD in complex with CS-tubulin and a microtubule -
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Basic information
Entry | Database: PDB / ID: 3j2u | ||||||
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Title | Kinesin-13 KLP10A HD in complex with CS-tubulin and a microtubule | ||||||
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![]() | MOTOR PROTEIN / tubulin / kinesin / kinesin-13 / KinI / depolymerase / depolymerization / microtubule / Kinesin13 | ||||||
Function / homology | ![]() establishment of mitotic spindle asymmetry / establishment of meiotic spindle orientation / plus-end specific microtubule depolymerization / asymmetric protein localization involved in cell fate determination / cortical microtubule / 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 / plus-end specific microtubule depolymerization / asymmetric protein localization involved in cell fate determination / cortical microtubule / 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 / microtubule motor activity / kinesin complex / spindle organization / microtubule-based movement / mitotic spindle pole / cytoskeletal motor activity / centrosome duplication / microtubule-based process / chromosome, centromeric region / mitotic spindle organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / spindle pole / microtubule cytoskeleton organization / spindle / microtubule cytoskeleton / mitotic cell cycle / nervous system development / microtubule binding / microtubule / protein heterodimerization activity / cell division / GTPase activity / centrosome / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 10.8 Å | ||||||
![]() | Asenjo, A.B. / Chatterjee, C. / Tan, D. / DePaoli, V. / Rice, W.J. / Diaz-Avalos, R. / Silvestry, M. / Sosa, H. | ||||||
![]() | ![]() 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 |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 393 KB | Display | ![]() |
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PDB format | ![]() | 312.8 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5565MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 42 / Rise per n subunits: 5.553 Å / Rotation per n subunits: 168.087 °) |
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Components
#1: Protein | Mass: 41810.918 Da / Num. of mol.: 1 / Fragment: head domain (UNP residues 279-615) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Protein | Mass: 50107.238 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 49907.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: kinesin-13 KLP10A head domain in complex with CS-tubulin and a microtubule Type: COMPLEX |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company | |||||||||||||||
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EM imaging | Date: May 1, 2012 / Electron source:
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Processing
EM software |
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CTF correction | Details: each particle | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 168.087 ° / Axial rise/subunit: 5.553 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 10.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54584 / Nominal pixel size: 2 Å / Actual pixel size: 2 Å / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: HELICAL | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Details: REFINEMENT PROTOCOL--RIGID BODY DETAILS--The domains were separately fitted with the global fitting option of the routine fitmap within UCSF-Chimera. Best fit was chosen based on the maximum ...Details: REFINEMENT PROTOCOL--RIGID BODY DETAILS--The domains were separately fitted with the global fitting option of the routine fitmap within UCSF-Chimera. Best fit was chosen based on the maximum cross-correlation value between the EM density and an 11 A resolution density model of the atomic structure of the domain to be fitted. | ||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Accession code: 1JFF / Initial refinement model-ID: 1 / PDB-ID: 1JFF / Source name: PDB / Type: experimental model
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Refinement step | Cycle: LAST
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