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- PDB-8yue: Crystal structure of the kinesin-14 motor protein from Drosophila... -

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Basic information

Entry
Database: PDB / ID: 8yue
TitleCrystal structure of the kinesin-14 motor protein from Drosophila melanogaster
ComponentsProtein claret segregational
KeywordsMOTOR PROTEIN / Kinesin-related / Microtubule motor protein / Spindle motor
Function / homology
Function and homology information


minus-end directed microtubule sliding / distributive segregation / regulation of mitotic spindle elongation / meiotic spindle assembly / mitotic spindle elongation / mitotic spindle microtubule / meiotic spindle organization / microtubule bundle formation / regulation of mitotic spindle assembly / mitotic centrosome separation ...minus-end directed microtubule sliding / distributive segregation / regulation of mitotic spindle elongation / meiotic spindle assembly / mitotic spindle elongation / mitotic spindle microtubule / meiotic spindle organization / microtubule bundle formation / regulation of mitotic spindle assembly / mitotic centrosome separation / meiotic spindle / spindle assembly involved in female meiosis / minus-end-directed microtubule motor activity / spindle organization / mitotic spindle assembly / mRNA transport / mitotic spindle organization / chromosome segregation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / spindle / microtubule binding / cell division / hydrolase activity / centrosome / protein homodimerization activity / ATP binding / nucleus / cytosol
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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Protein claret segregational
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsWei, Y. / Jobichen, C. / Imasaki, T. / Nitta, R. / Wang, M.Y. / Sivaraman, J. / Endow, S.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)1R21HD105034-01A1 United States
CitationJournal: Sci Rep / Year: 2026
Title: Structural analysis of a motor with increased mechanical output reveals new transitions in kinesin microtubule motility.
Authors: Satoki Shibata / Matthew Y Wang / Tsuyoshi Imasaki / Hideki Shigematsu / Diego Ugarte La Torre / Yuanyuan Wei / Chacko Jobichen / Hajime Hagio / J Sivaraman / Yuji Sugita / Sharyn A Endow / Ryo Nitta /
Abstract: Kinesin motors use ATP to produce force in cells, yet the conformational changes that generate force remain uncertain. Here, we report structural and mechanistic insights into a minus-end-directed ...Kinesin motors use ATP to produce force in cells, yet the conformational changes that generate force remain uncertain. Here, we report structural and mechanistic insights into a minus-end-directed kinesin-14 that exhibits increased mechanical output – the variant motor binds microtubules more tightly and moves with faster velocity than wild type. High-resolution structures, together with molecular dynamics simulations, reveal previously unobserved transitions in the nucleotide hydrolysis cycle. ADP release, triggered by microtubule binding, is coupled to twisting of the central β-sheet and stabilization of the stalk prior to the power stroke. ATP binding induces stalk fluctuations and a swing of the neck mimic, an element analogous to the kinesin-1 neck linker, resembling neck linker docking in plus-end-directed kinesins. The power stroke, characterized by a large stalk rotation, is followed by motor detachment from microtubules. The subsequent recovery stroke occurs while the motor is bound to ADP and free Pi, accompanied by β-strand-to-loop transitions, or β-sheet melting, implying that β-sheet refolding facilitates Pi release. The observed twisting and melting identify the central β-sheet as the long-sought elastic element or spring required for motor force production. The transitions we observe in kinesin-14 may also apply to other kinesins – this remains to be tested.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-28573-7.
History
DepositionMar 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein claret segregational
B: Protein claret segregational
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1478
Polymers88,9132
Non-polymers1,2346
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-75 kcal/mol
Surface area34250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.506, 67.617, 94.196
Angle α, β, γ (deg.)90.00, 96.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein claret segregational / Kinesin-14


Mass: 44456.441 Da / Num. of mol.: 2 / Mutation: Y485K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: ncd, CA(ND), CG7831
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P20480, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.5M NaCl, 50mM NaPi, pH6.8, 7mM DTT, 13% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→93.5 Å / Num. obs: 17466 / % possible obs: 96.1 % / Redundancy: 6.6 % / Rpim(I) all: 0.138 / Net I/σ(I): 6.9
Reflection shellResolution: 3.1→3.32 Å / Num. unique obs: 2747 / Rpim(I) all: 1

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→46.75 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2947 874 5 %
Rwork0.251 --
obs0.2532 17466 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→46.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5773 0 20 0 5793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0185899
X-RAY DIFFRACTIONf_angle_d1.5747964
X-RAY DIFFRACTIONf_dihedral_angle_d9.513795
X-RAY DIFFRACTIONf_chiral_restr0.075898
X-RAY DIFFRACTIONf_plane_restr0.0191024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.350.4251300.43092484X-RAY DIFFRACTION88
3.35-3.610.36511480.36572787X-RAY DIFFRACTION99
3.61-3.970.33311450.32082770X-RAY DIFFRACTION98
3.97-4.540.32561490.24212825X-RAY DIFFRACTION100
4.54-5.720.30971480.23772824X-RAY DIFFRACTION99
5.72-46.750.23761540.20082902X-RAY DIFFRACTION99

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