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

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Basic information

Entry
Database: PDB / ID: 4pxu
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 / MOLECULAR REPLACEMENT / Resolution: 2.601 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
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5853
Polymers48,4672
Non-polymers1181
Water1,08160
1
A: Bipolar kinesin KRP-130
B: Bipolar kinesin KRP-130
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)97,1706
Polymers96,9344
Non-polymers2362
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area22410 Å2
ΔGint-210 kcal/mol
Surface area33660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.648, 138.648, 105.792
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: 24233.400 Da / Num. of mol.: 2 / Fragment: Bipolar assembly domain of kinesin-5 (Klp61f)
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
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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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: 3.03 Å3/Da / Density % sol: 59.38 %
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: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2013 / Details: K-B focusing mirrors
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.601→40.024 Å / Num. all: 18960 / Num. obs: 15885 / % possible obs: 83.84 % / Observed criterion σ(F): 1.36 / Observed criterion σ(I): 2.3 / Redundancy: 8.2 % / Biso Wilson estimate: 75.9 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.111 / Net I/σ(I): 10.8
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.989 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2694 / Rsym value: 0.966 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4PXT

4pxt


Resolution: 2.601→40.024 Å / SU ML: 0.31 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): 2.3 / Phase error: 30.36 / Stereochemistry target values: ML / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.252 785 4.94 %RANDOM
Rwork0.2229 ---
obs0.2244 15885 83.84 %-
all-18960 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.55 Å2
Baniso -1Baniso -2Baniso -3
1--2.65 Å20 Å20 Å2
2---2.65 Å20 Å2
3---5.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.601→40.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2287 0 8 60 2355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062307
X-RAY DIFFRACTIONf_angle_d0.8623079
X-RAY DIFFRACTIONf_dihedral_angle_d15.583929
X-RAY DIFFRACTIONf_chiral_restr0.033346
X-RAY DIFFRACTIONf_plane_restr0.004409
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.6011-2.7640.3674230.27531097112036
2.764-2.97730.3287940.2352047214170
2.9773-3.27680.29891560.25132823297996
3.2768-3.75070.28611780.218629463124100
3.7507-4.72430.22831750.193229973172100
4.7243-40.02890.221590.233431903349100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6141-0.4186-1.17680.3622-0.15350.71860.2886-0.2332-0.4893-0.0228-0.12620.0621-0.0135-0.109-0.11610.2595-0.03710.05070.4789-0.05180.2841-20.05879.30154.8571
21.12240.9697-0.39651.0361-0.41680.16520.14150.24930.4884-0.4651-0.1885-0.0947-0.17310.23680.09771.0725-0.2980.2581.5758-0.14791.634694.70816.3369-21.3902
34.66110.0857-0.79770.5572-0.09760.51080.4284-0.22460.4496-0.0033-0.2329-0.0622-0.08320.0439-0.06040.2632-0.02060.07160.4449-0.02290.2655-0.833813.69822.6439
43.703-3.0949-0.57457.10295.36565.37180.0022.643-0.8303-1.08810.2052-0.56320.13130.3306-0.03280.7663-0.02520.32551.60360.03781.418-93.3133.704323.4516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 640 through 791 )
2X-RAY DIFFRACTION2chain 'B' and (resid 660 through 668 )
3X-RAY DIFFRACTION3chain 'B' and (resid 669 through 790 )
4X-RAY DIFFRACTION4chain 'B' and (resid 791 through 795 )

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