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- PDB-9l6k: Crystal structure of nucleotide-free human kinesin-1 motor domain... -

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Basic information

Entry
Database: PDB / ID: 9l6k
TitleCrystal structure of nucleotide-free human kinesin-1 motor domain (G234V 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 / cytolytic granule membrane / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / mitocytosis / retrograde neuronal dense core vesicle transport / anterograde axonal protein transport / ciliary rootlet ...regulation of modification of synapse structure, modulating synaptic transmission / plus-end-directed vesicle transport along microtubule / cytoplasm organization / cytolytic granule membrane / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / mitocytosis / retrograde neuronal dense core vesicle transport / anterograde axonal protein transport / ciliary rootlet / lysosome localization / positive regulation of potassium ion transport / plus-end-directed microtubule motor activity / Kinesins / RHO GTPases activate KTN1 / vesicle transport along microtubule / kinesin complex / microtubule motor activity / mitochondrion transport along microtubule / centrosome localization / COPI-dependent Golgi-to-ER retrograde traffic / stress granule disassembly / natural killer cell mediated cytotoxicity / microtubule-based movement / Insulin processing / synaptic vesicle transport / postsynaptic cytosol / phagocytic vesicle / sperm end piece / axon cytoplasm / MHC class II antigen presentation / dendrite cytoplasm / axon guidance / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / regulation of membrane potential / cellular response to type II interferon / centriolar satellite / Signaling by ALK fusions and activated point mutants / nuclear membrane / microtubule binding / vesicle / microtubule / cadherin binding / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / membrane / cytoplasm / 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
Kinesin-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 24, 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)76,6682
Polymers76,6682
Non-polymers00
Water00
1
A: Kinesin-1 heavy chain


Theoretical massNumber of molelcules
Total (without water)38,3341
Polymers38,3341
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kinesin-1 heavy chain


Theoretical massNumber of molelcules
Total (without water)38,3341
Polymers38,3341
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.120, 162.370, 53.200
Angle α, β, γ (deg.)90.000, 114.497, 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: 38334.027 Da / Num. of mol.: 2 / Mutation: G234V
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
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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 20% PEG 3350, 100mM HEPES-NaOH, 200mM ammonium acetate, 3% xylitol
PH range: 7.7-8.0

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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: Dec 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→19.5 Å / Num. obs: 16383 / % possible obs: 97.6 % / Redundancy: 7.14 % / Biso Wilson estimate: 25.21 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 29.58
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.081 / Mean I/σ(I) obs: 13.25 / Num. unique obs: 1011 / % possible all: 85.6

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.49 Å / SU ML: 0.3184 / Cross valid method: FREE R-VALUE / σ(F): 2.07 / Phase error: 24.1718
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2582 824 5.03 %
Rwork0.2003 15559 -
obs0.2033 16383 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.47 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5017 0 0 0 5017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00285091
X-RAY DIFFRACTIONf_angle_d0.53936860
X-RAY DIFFRACTIONf_chiral_restr0.0442781
X-RAY DIFFRACTIONf_plane_restr0.0038886
X-RAY DIFFRACTIONf_dihedral_angle_d14.29591916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.980.28411250.2332340X-RAY DIFFRACTION89.51
2.98-3.20.32111270.24012625X-RAY DIFFRACTION99.96
3.2-3.520.28971420.2252653X-RAY DIFFRACTION100
3.52-4.030.26361480.1982627X-RAY DIFFRACTION100
4.03-5.060.22541260.16632660X-RAY DIFFRACTION100
5.06-19.490.20871560.18022654X-RAY DIFFRACTION100

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