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- PDB-9l78: Crystal structure of nucleotide-free human kinesin-1 motor domain... -

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Basic information

Entry
Database: PDB / ID: 9l78
TitleCrystal structure of nucleotide-free human kinesin-1 motor domain (G234A mutant)
ComponentsKinesin-1 heavy chain
KeywordsMOTOR PROTEIN / Kinesin
Function / homology
Function and homology information


regulation of modification of synapse structure, modulating synaptic transmission / plus-end-directed vesicle transport along microtubule / cytoplasm organization / anterograde dendritic transport of neurotransmitter receptor complex / cytolytic granule membrane / anterograde neuronal dense core vesicle transport / mitocytosis / retrograde neuronal dense core vesicle transport / anterograde axonal protein transport / vesicle transport along microtubule ...regulation of modification of synapse structure, modulating synaptic transmission / plus-end-directed vesicle transport along microtubule / cytoplasm organization / anterograde dendritic transport of neurotransmitter receptor complex / cytolytic granule membrane / anterograde neuronal dense core vesicle transport / mitocytosis / retrograde neuronal dense core vesicle transport / anterograde axonal protein transport / vesicle transport along microtubule / lysosome localization / positive regulation of potassium ion transport / plus-end-directed microtubule motor activity / Kinesins / RHO GTPases activate KTN1 / kinesin complex / microtubule motor activity / centrosome localization / mitochondrion transport along microtubule / COPI-dependent Golgi-to-ER retrograde traffic / ciliary rootlet / microtubule-based movement / natural killer cell mediated cytotoxicity / stress granule disassembly / synaptic vesicle transport / Insulin processing / postsynaptic cytosol / phagocytic vesicle / axon cytoplasm / dendrite cytoplasm / MHC class II antigen presentation / axon guidance / regulation of membrane potential / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / cellular response to type II interferon / centriolar satellite / Signaling by ALK fusions and activated point mutants / microtubule binding / nuclear membrane / vesicle / microtubule / cadherin binding / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / membrane / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Kinesin-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsMakino, T. / Miyazono, K. / Tanokura, M. / Tomishige, M.
Funding support France, 1items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)RGY62/2006 France
CitationJournal: J Cell Biol / Year: 2025
Title: Tension-induced suppression of allosteric conformational changes coordinates kinesin-1 stepping.
Authors: Tsukasa Makino / Ryo Kanada / Teppei Mori / Ken-Ichi Miyazono / Yuta Komori / Haruaki Yanagisawa / Shoji Takada / Masaru Tanokura / Masahide Kikkawa / Michio Tomishige /
Abstract: Kinesin-1 walks along microtubules by alternating ATP hydrolysis and movement of its two motor domains ("head"). The detached head preferentially binds to the forward tubulin-binding site after ATP ...Kinesin-1 walks along microtubules by alternating ATP hydrolysis and movement of its two motor domains ("head"). The detached head preferentially binds to the forward tubulin-binding site after ATP binds to the microtubule-bound head, but the mechanism preventing premature microtubule binding while the partner head awaits ATP remains unknown. Here, we examined the role of the neck linker, the segment connecting two heads, in this mechanism. Structural analyses of the nucleotide-free head revealed a bulge just ahead of the neck linker's base, creating an asymmetric constraint on its mobility. While the neck linker can stretch freely backward, it must navigate around this bulge to extend forward. We hypothesized that increased neck linker tension suppresses premature binding of the tethered head, which was supported by molecular dynamics simulations and single-molecule fluorescence assays. These findings demonstrate a tension-dependent allosteric mechanism that coordinates the movement of two heads, where neck linker tension modulates the allosteric conformational changes rather than directly affecting the nucleotide state.
History
DepositionDec 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinesin-1 heavy chain
B: Kinesin-1 heavy chain


Theoretical massNumber of molelcules
Total (without water)76,6122
Polymers76,6122
Non-polymers00
Water181
1
A: Kinesin-1 heavy chain


Theoretical massNumber of molelcules
Total (without water)38,3061
Polymers38,3061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kinesin-1 heavy chain


Theoretical massNumber of molelcules
Total (without water)38,3061
Polymers38,3061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.220, 156.900, 52.960
Angle α, β, γ (deg.)90.000, 114.556, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Kinesin-1 heavy chain / Conventional kinesin heavy chain / Ubiquitous kinesin heavy chain / UKHC


Mass: 38305.973 Da / Num. of mol.: 2 / Mutation: G234A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF5B, KNS, KNS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P33176
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20 % PEG 3350, 100mM HEPES-NaOH, 200mM ammonium acetate, 3% xylitol, pH 7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.82→20 Å / Num. obs: 15132 / % possible obs: 95.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 26.56 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.13
Reflection shellResolution: 2.82→2.9 Å / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 4.96 / Num. unique obs: 653

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.82→19.58 Å / SU ML: 0.4086 / Cross valid method: FREE R-VALUE / σ(F): 2.11 / Phase error: 24.0345
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2653 757 5 %
Rwork0.2068 14372 -
obs0.2097 15129 96.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.21 Å2
Refinement stepCycle: LAST / Resolution: 2.82→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4761 0 0 1 4762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00384833
X-RAY DIFFRACTIONf_angle_d0.60656507
X-RAY DIFFRACTIONf_chiral_restr0.0446736
X-RAY DIFFRACTIONf_plane_restr0.0047838
X-RAY DIFFRACTIONf_dihedral_angle_d15.65651819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-3.040.31441290.24612451X-RAY DIFFRACTION82.9
3.04-3.350.35641570.23782986X-RAY DIFFRACTION99.87
3.35-3.830.27551550.20872945X-RAY DIFFRACTION99.68
3.83-4.810.23171580.18423000X-RAY DIFFRACTION99.81
4.81-19.580.20781580.19172990X-RAY DIFFRACTION99.94

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