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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 / 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: 2.82 Å
AuthorsMakino, T. / Miyazono, K. / Tanokura, M. / Tomishige, M.
Funding support France, 1items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)RGY62/2006 France
CitationJournal: 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 26, 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)76,6122
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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