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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
TitleKinesin-13 KLP10A HD in complex with CS-tubulin and a microtubule
Components
  • Kinesin-like protein Klp10A
  • Tubulin alpha-1A chain
  • Tubulin beta-2B chain
KeywordsMOTOR PROTEIN / tubulin / kinesin / kinesin-13 / KinI / depolymerase / depolymerization / microtubule / Kinesin13
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 10.8 Å
AuthorsAsenjo, A.B. / Chatterjee, C. / Tan, D. / DePaoli, V. / Rice, W.J. / 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 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Jul 18, 2018Group: Author supporting evidence / Data collection
Category: em_image_scans / em_single_particle_entity / em_software
Item: _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details

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Structure visualization

Movie
  • Biological unit as representative helical assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-5565
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  • Superimposition on EM map
  • EMDB-5565
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
K: Kinesin-like protein Klp10A
A: Tubulin alpha-1A chain
B: Tubulin beta-2B chain
C: Tubulin alpha-1A chain
D: Tubulin beta-2B chain


Theoretical massNumber of molelcules
Total (without water)241,8415
Polymers241,8415
Non-polymers00
Water0
1
K: Kinesin-like protein Klp10A
A: Tubulin alpha-1A chain
B: Tubulin beta-2B chain
C: Tubulin alpha-1A chain
D: Tubulin beta-2B chain
x 42


Theoretical massNumber of molelcules
Total (without water)10,157,319210
Polymers10,157,319210
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation41
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical 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 Kinesin-like protein Klp10A / Kinesin-like protein at cytological position 10A


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.) Drosophila melanogaster (fruit fly) / Gene: Klp10A, CG1453 / Production host: Escherichia coli (E. coli) / References: UniProt: Q960Z0
#2: Protein Tubulin alpha-1A chain / / Alpha-tubulin 1 / Tubulin alpha-1 chain


Mass: 50107.238 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: brain / References: UniProt: P81947
#3: Protein Tubulin beta-2B chain


Mass: 49907.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: brain / References: UniProt: Q6B856

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: kinesin-13 KLP10A head domain in complex with CS-tubulin and a microtubule
Type: COMPLEX
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
EM imaging

Date: May 1, 2012 / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Mode: BRIGHT FIELDBright-field microscopy / Specimen-ID: 1

IDAccelerating voltage (kV)ModelSpecimen holder modelSpecimen holder type
1300JEOL 3200FSCJEOLJEOL
2200FEI TECNAI F20GATAN LIQUID NITROGENGATAN LIQUID NITROGEN

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Processing

EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2UCSF Chimeramodel fitting
3Custom3D reconstruction
4IHRSR3D reconstruction
5SPIDER3D reconstruction
CTF correctionDetails: each particle
Helical symmertyAngular rotation/subunit: 168.087 ° / Axial rise/subunit: 5.553 Å / Axial symmetry: C1
3D reconstructionResolution: 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 buildingProtocol: 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

1jff

/ Source name: PDB / Type: experimental model

IDPdb chain-ID
1A
2B
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms15575 0 0 0 15575

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