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- PDB-4y05: KIF2C short Loop2 construct -

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Basic information

Entry
Database: PDB / ID: 4y05
TitleKIF2C short Loop2 construct
ComponentsKinesin-like protein KIF2C
KeywordsTRANSPORT PROTEIN / KINESIN-13 / MICROTUBULE / TUBULIN
Function / homology
Function and homology information


regulation of chromosome segregation / establishment or maintenance of microtubule cytoskeleton polarity / metaphase chromosome alignment / microtubule plus-end / centromeric DNA binding / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / Kinesins / microtubule depolymerization / COPI-dependent Golgi-to-ER retrograde traffic ...regulation of chromosome segregation / establishment or maintenance of microtubule cytoskeleton polarity / metaphase chromosome alignment / microtubule plus-end / centromeric DNA binding / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / Kinesins / microtubule depolymerization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / mitotic metaphase chromosome alignment / microtubule-based movement / chromosome, centromeric region / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / MHC class II antigen presentation / RHO GTPases Activate Formins / kinetochore / spindle / Separation of Sister Chromatids / microtubule cytoskeleton / microtubule binding / microtubule / cell division / centrosome / ATP hydrolysis activity / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
Kinesin motor domain / Kinesin / 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 ...Kinesin motor domain / Kinesin / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Kinesin-like protein KIF2C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.59 Å
AuthorsWang, W. / Knossow, M. / Gigant, B.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: New Insights into the Coupling between Microtubule Depolymerization and ATP Hydrolysis by Kinesin-13 Protein Kif2C.
Authors: Wang, W. / Shen, T. / Guerois, R. / Zhang, F. / Kuerban, H. / Lv, Y. / Gigant, B. / Knossow, M. / Wang, C.
History
DepositionFeb 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Aug 5, 2015Group: Database references
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinesin-like protein KIF2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1736
Polymers43,4341
Non-polymers7405
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-50 kcal/mol
Surface area15030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.889, 83.889, 147.872
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Kinesin-like protein KIF2C / Kinesin-like protein 6 / Mitotic centromere-associated kinesin / MCAK


Mass: 43433.555 Da / Num. of mol.: 1 / Fragment: UNP residues 216-599
Mutation: R330A R379A P294deleted K295deleted L296deleted L300deleted T301deleted K302deleted
Source method: isolated from a genetically manipulated source
Details: The construct has a C-terminal His-tag. / Source: (gene. exp.) Homo sapiens (human) / Gene: KIF2C, KNSL6 / Plasmid: PET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99661
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M AMMONIUM SULFATE, 10% ETHYLENEGLYCOL, 0.1M TRIS-HCL PH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.59→42.5 Å / Num. all: 17175 / Num. obs: 17174 / % possible obs: 99.7 % / Redundancy: 13.6 % / Biso Wilson estimate: 95.27 Å2 / Rpim(I) all: 0.015 / Rrim(I) all: 0.054 / Rsym value: 0.053 / Net I/av σ(I): 8.663 / Net I/σ(I): 27.6 / Num. measured all: 234047
Reflection shellResolution: 2.59→2.73 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 2.4 / Num. measured all: 7349 / Num. unique all: 643 / Rpim(I) all: 0.009 / Rsym value: 1.22 / Net I/σ(I) obs: 75.8 / Rejects: 0 / % possible all: 98

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASERphasing
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HEH

2heh


Resolution: 2.59→24.72 Å / Cor.coef. Fo:Fc: 0.9542 / Cor.coef. Fo:Fc free: 0.9524 / SU R Cruickshank DPI: 0.313 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.329 / SU Rfree Blow DPI: 0.208 / SU Rfree Cruickshank DPI: 0.206
RfactorNum. reflection% reflectionSelection details
Rfree0.2042 871 5.1 %RANDOM
Rwork0.1922 ---
obs0.1928 17069 99.94 %-
Displacement parametersBiso max: 218.81 Å2 / Biso mean: 103.11 Å2 / Biso min: 55.38 Å2
Baniso -1Baniso -2Baniso -3
1--5.1664 Å20 Å20 Å2
2---5.1664 Å20 Å2
3---10.3329 Å2
Refine analyzeLuzzati coordinate error obs: 0.496 Å
Refinement stepCycle: final / Resolution: 2.59→24.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 43 52 2607
Biso mean--130.49 82.01 -
Num. residues----330
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d906SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes397HARMONIC5
X-RAY DIFFRACTIONt_it2619HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion354SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2933SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2619HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3549HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion18.83
LS refinement shellResolution: 2.59→2.75 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2548 162 6.02 %
Rwork0.2311 2531 -
all0.2326 2693 -
obs--99.94 %
Refinement TLS params.Method: refined / Origin x: 7.5833 Å / Origin y: -19.2571 Å / Origin z: 15.2363 Å
111213212223313233
T-1.0823 Å2-0.006 Å20.0548 Å2--0.794 Å2-0.1091 Å2---0.9413 Å2
L4.5735 °21.4028 °23.6805 °2-2.5009 °22.8629 °2--7.1725 °2
S-0.0728 Å °0.8316 Å °-0.4469 Å °-0.1564 Å °0.4367 Å °-0.3306 Å °-0.2602 Å °0.4913 Å °-0.3639 Å °
Refinement TLS groupSelection details: { A|* }

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