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- PDB-6igv: Kif5b stalk I coiled-coil -

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Basic information

Entry
Database: PDB / ID: 6igv
TitleKif5b stalk I coiled-coil
ComponentsKinesin-1 heavy chain
KeywordsMOTOR PROTEIN / coiled-coil
Function / homology
Function and homology information


RHO GTPases activate KTN1 / membrane-bounded organelle / cytoplasm organization / plus-end-directed vesicle transport along microtubule / anterograde dendritic transport of neurotransmitter receptor complex / positive regulation of voltage-gated sodium channel activity / Kinesins / positive regulation of vesicle fusion / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport ...RHO GTPases activate KTN1 / membrane-bounded organelle / cytoplasm organization / plus-end-directed vesicle transport along microtubule / anterograde dendritic transport of neurotransmitter receptor complex / positive regulation of voltage-gated sodium channel activity / Kinesins / positive regulation of vesicle fusion / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / vesicle transport along microtubule / cytoskeleton-dependent intracellular transport / positive regulation of intracellular protein transport / lysosome localization / positive regulation of potassium ion transport / MHC class II antigen presentation / natural killer cell mediated cytotoxicity / JUN kinase binding / plus-end-directed microtubule motor activity / stress granule disassembly / ciliary rootlet / centrosome localization / microtubule lateral binding / microtubule motor activity / kinesin complex / synaptic vesicle transport / mitochondrial transport / microtubule-based movement / positive regulation of insulin secretion involved in cellular response to glucose stimulus / microtubule-based process / centriolar satellite / endocytic vesicle / axonal growth cone / axon cytoplasm / dendrite cytoplasm / phagocytic vesicle / regulation of membrane potential / positive regulation of synaptic transmission, GABAergic / hippocampus development / positive regulation of protein localization to plasma membrane / axon guidance / cellular response to type II interferon / microtubule cytoskeleton / microtubule binding / microtubule / vesicle / neuron projection / lysosomal membrane / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / identical protein binding / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.999 Å
AuthorsZhang, S.J. / Sun, W.p. / Kong, B.
CitationJournal: To Be Published
Title: Kif5b stalk I coiled-coil
Authors: Zhang, S.J. / Sun, W.p. / Kong, B.
History
DepositionSep 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinesin-1 heavy chain


Theoretical massNumber of molelcules
Total (without water)13,5851
Polymers13,5851
Non-polymers00
Water00
1
A: Kinesin-1 heavy chain

A: Kinesin-1 heavy chain


Theoretical massNumber of molelcules
Total (without water)27,1702
Polymers27,1702
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_557x,-y+1/2,-z+9/41
Buried area5050 Å2
ΔGint-42 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.620, 84.620, 313.912
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

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


Mass: 13585.194 Da / Num. of mol.: 1 / Fragment: UNP residues 446-563
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif5b, Khcs, Kns1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q61768

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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: 10.34 Å3/Da / Density % sol: 88.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.2M Ammonium Sulfate, 40%MPD, 0.1M sodium cacodylate pH6.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97778 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97778 Å / Relative weight: 1
ReflectionResolution: 2.999→50 Å / Num. obs: 15845 / % possible obs: 83.91 % / Redundancy: 18.5 % / CC1/2: 0.988 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.041 / Net I/σ(I): 15.9
Reflection shellResolution: 3→3.05 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 4.68 / Num. unique obs: 11994 / CC1/2: 0.968 / Rpim(I) all: 0.214 / % possible all: 37.75

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Processing

Software
NameVersionClassification
PHENIX1.14_3228refinement
HKL-2000data reduction
HKL-2000data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.999→37.571 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3088 1554 9.94 %
Rwork0.2861 14079 -
obs0.2886 15633 71.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.98 Å2 / Biso mean: 23.1356 Å2 / Biso min: 1.55 Å2
Refinement stepCycle: final / Resolution: 2.999→37.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms945 0 0 0 945
Num. residues----118
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.999-3.09560.3165500.276443225
3.0956-3.20620.2849560.29456231
3.2062-3.33450.3834860.351273041
3.3345-3.48610.34931090.3384100356
3.4861-3.66980.27841420.3121122969
3.6698-3.89950.30331490.2773138377
3.8995-4.20020.34991830.2675163892
4.2002-4.62220.26861910.23841781100
4.6222-5.28940.27522040.2581789100
5.2894-6.65810.36981910.36361789100
6.6581-37.5710.31531930.2934174397

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