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- PDB-4pxt: Structural basis for the assembly of the mitotic motor kinesin-5 ... -

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Basic information

Entry
Database: PDB / ID: 4pxt
TitleStructural basis for the assembly of the mitotic motor kinesin-5 into bipolar tetramers
ComponentsBipolar kinesin KRP-130
KeywordsCELL CYCLE / Coiled-coil / Bipolar assembly domain of kinesin-5 / bipolar tetramers / anti-parallel four-helix bundle / Kinesin-5 functions via a "sliding filament" mechanism / crosslinking adjacent microtubules into bundles throughout the mitotic spindle / Microtubules
Function / homology
Function and homology information


aster / plus-end directed microtubule sliding / fusome organization / fusome / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / centrosome separation / spindle elongation / mitotic spindle microtubule / positive regulation of Golgi to plasma membrane protein transport ...aster / plus-end directed microtubule sliding / fusome organization / fusome / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / centrosome separation / spindle elongation / mitotic spindle microtubule / positive regulation of Golgi to plasma membrane protein transport / microtubule bundle formation / plus-end-directed microtubule motor activity / mitotic centrosome separation / microtubule associated complex / kinesin complex / microtubule-based movement / mitotic spindle pole / Golgi organization / cytoskeletal motor activity / protein secretion / mitotic spindle assembly / mitotic spindle organization / spindle microtubule / mitotic spindle / spindle / mitotic cell cycle / microtubule binding / microtubule / cell division / Golgi apparatus / endoplasmic reticulum / ATP binding / nucleus / cytoplasm
Similarity search - Function
Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / 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-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / 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-like protein Klp61F
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsScholey, J.E. / Nithianantham, S. / Scholey, J.M. / Al-Bassam, J.
CitationJournal: Elife / Year: 2014
Title: Structural basis for the assembly of the mitotic motor Kinesin-5 into bipolar tetramers.
Authors: Scholey, J.E. / Nithianantham, S. / Scholey, J.M. / Al-Bassam, J.
History
DepositionMar 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bipolar kinesin KRP-130
B: Bipolar kinesin KRP-130


Theoretical massNumber of molelcules
Total (without water)49,9672
Polymers49,9672
Non-polymers00
Water0
1
A: Bipolar kinesin KRP-130
B: Bipolar kinesin KRP-130

A: Bipolar kinesin KRP-130
B: Bipolar kinesin KRP-130


Theoretical massNumber of molelcules
Total (without water)99,9354
Polymers99,9354
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area25570 Å2
ΔGint-220 kcal/mol
Surface area36000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.070, 139.070, 104.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Bipolar kinesin KRP-130 / Kinesin-like protein Klp61F


Mass: 24983.721 Da / Num. of mol.: 2 / Fragment: Bipolar assembly domain of kinesin-5 (Klp61f) / Mutation: H836G, H836S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Strain: Drosophila melanogaster / Gene: CG9191, KLP2, Klp61F, Klp61F or DmKlp61F or CG9191 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P46863

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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: 2.91 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 4-6 % (+/-) 2-Methyl-2,4 pentanediol (MPD), 100mM MES, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: 6-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 7, 2013 / Details: flat collimating Rh coated mirror
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→60.219 Å / Num. all: 13704 / Num. obs: 12639 / % possible obs: 92.37 % / Observed criterion σ(F): 1.99 / Observed criterion σ(I): 3.5 / Redundancy: 11.1 % / Biso Wilson estimate: 54.95 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.124 / Net I/σ(I): 11.9
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1940 / Rsym value: 0.683 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→60.219 Å / SU ML: 0.38 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 1.99 / σ(I): 3.5 / Phase error: 28.06 / Stereochemistry target values: ML / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.2735 610 4.83 %RANDOM
Rwork0.2416 ---
obs0.2431 12639 92.37 %-
all-13704 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.67 Å2
Baniso -1Baniso -2Baniso -3
1--4.9 Å20 Å20 Å2
2---4.9 Å20 Å2
3---9.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 2.9→60.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 0 0 2518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062532
X-RAY DIFFRACTIONf_angle_d0.8873379
X-RAY DIFFRACTIONf_dihedral_angle_d17.1781019
X-RAY DIFFRACTIONf_chiral_restr0.03380
X-RAY DIFFRACTIONf_plane_restr0.003451
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.9004-3.19220.33351170.29712173229069
3.1922-3.65410.31011680.286831873355100
3.6541-4.60350.27431630.232532433406100
4.6035-60.2320.24131620.216334263588100

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