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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 / anterograde dendritic transport of neurotransmitter receptor complex / cytolytic granule membrane / mitocytosis / anterograde neuronal dense core vesicle transport / 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 / mitocytosis / anterograde neuronal dense core vesicle transport / 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 / RHO GTPases activate KTN1 / Kinesins / kinesin complex / microtubule motor activity / centrosome localization / COPI-dependent Golgi-to-ER retrograde traffic / mitochondrion transport along microtubule / ciliary rootlet / microtubule-based movement / natural killer cell mediated cytotoxicity / stress granule disassembly / synaptic vesicle transport / Insulin processing / postsynaptic cytosol / centriolar satellite / 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 / Signaling by ALK fusions and activated point mutants / microtubule binding / 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: 2.8 Å
AuthorsMakino, T. / Miyazono, K. / Tanokura, M. / Tomishige, M.
Funding support France, 1items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)RGY62/2006 France
CitationJournal: Biorxiv / Year: 2024
Title: Tension-induced suppression of allosteric conformational changes coordinates kinesin-1 stepping
Authors: Makino, T. / Kanada, R. / Mori, T. / Miyazono, K.I. / Komori, Y. / Yanagisawa, H. / Takada, S. / Tanokura, M. / Kikkawa, M. / Tomishige, M.
History
DepositionDec 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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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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