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- PDB-6gr9: Human AURKC INCENP complex bound to VX-680 -

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Basic information

Entry
Database: PDB / ID: 6gr9
TitleHuman AURKC INCENP complex bound to VX-680
Components
  • Aurora kinase C
  • Inner centromere protein
KeywordsTRANSFERASE / Kinase / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


meiotic spindle midzone / meiotic spindle midzone assembly / central element / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / attachment of spindle microtubules to kinetochore ...meiotic spindle midzone / meiotic spindle midzone assembly / central element / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / attachment of spindle microtubules to kinetochore / chromocenter / lateral element / spindle pole centrosome / chromosome passenger complex / positive regulation of cytokinesis / mitotic cytokinesis / SUMOylation of DNA replication proteins / chromosome, centromeric region / mitotic spindle assembly / spindle midzone / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / pericentric heterochromatin / condensed chromosome / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization / regulation of cytokinesis / molecular function activator activity / meiotic cell cycle / chromosome segregation / spindle microtubule / RHO GTPases Activate Formins / kinetochore / spindle / Separation of Sister Chromatids / microtubule cytoskeleton / mitotic cell cycle / midbody / microtubule / nuclear body / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Inner centromere protein, ARK-binding domain / Chromosome passenger complex (CPC) protein INCENP N-terminal / Inner centromere protein, ARK binding region / Chromosome passenger complex (CPC) protein INCENP N terminal / Aurora kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...Inner centromere protein, ARK-binding domain / Chromosome passenger complex (CPC) protein INCENP N-terminal / Inner centromere protein, ARK binding region / Chromosome passenger complex (CPC) protein INCENP N terminal / Aurora kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-VX6 / Inner centromere protein / Aurora kinase C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsAbdul Azeez, K.R. / Sorrell, F.J. / von Delft, F. / Bountra, C. / Knapp, S. / Edwards, A.M. / Arrowsmith, C. / Elkins, J.M.
CitationJournal: To Be Published
Title: AURKC INCENP complex bound to BRD-7880
Authors: Abdul Azeez, K.R. / Elkins, J.M.
History
DepositionJun 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aurora kinase C
B: Inner centromere protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0304
Polymers40,4702
Non-polymers5612
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-50 kcal/mol
Surface area15710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.617, 82.617, 121.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Aurora kinase C / Aurora 3 / Aurora/IPL1-related kinase 3 / Aurora-related kinase 3 / Aurora/IPL1/Eg2 protein 2 / ...Aurora 3 / Aurora/IPL1-related kinase 3 / Aurora-related kinase 3 / Aurora/IPL1/Eg2 protein 2 / Serine/threonine-protein kinase 13 / Serine/threonine-protein kinase aurora-C


Mass: 32167.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AURKC, AIE2, AIK3, AIRK3, ARK3, STK13 / Plasmid: pHTvAmp1-SGC / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UQB9, non-specific serine/threonine protein kinase
#2: Protein Inner centromere protein


Mass: 8302.374 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INCENP / Plasmid: pHTvAmp1-SGC / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NQS7
#3: Chemical ChemComp-VX6 / CYCLOPROPANECARBOXYLIC ACID {4-[4-(4-METHYL-PIPERAZIN-1-YL)-6-(5-METHYL-2H-PYRAZOL-3-YLAMINO)-PYRIMIDIN-2-YLSULFANYL]-PHENYL}-AMIDE


Mass: 464.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28N8OS / Comment: inhibitor*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 % PEG3350, 10 % ethylene glycol, 0.1 M bis-tris-propane pH 7.5, 0.2 M sodium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Sep 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.25→71.55 Å / Num. obs: 23264 / % possible obs: 100 % / Redundancy: 5.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.8
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2 / Num. unique obs: 2104 / CC1/2: 0.689 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GR8

6gr8


Resolution: 2.25→71.55 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.178 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.184 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22443 1177 5.1 %RANDOM
Rwork0.18165 ---
obs0.18379 22049 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.179 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0.19 Å20 Å2
2---0.38 Å2-0 Å2
3---1.23 Å2
Refinement stepCycle: 1 / Resolution: 2.25→71.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 38 162 2805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0142723
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172472
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.6743708
X-RAY DIFFRACTIONr_angle_other_deg0.8241.6285790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4655318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25620.621145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68515460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9031523
X-RAY DIFFRACTIONr_chiral_restr0.0620.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02497
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9694.3611269
X-RAY DIFFRACTIONr_mcbond_other2.974.3571268
X-RAY DIFFRACTIONr_mcangle_it4.4996.5111582
X-RAY DIFFRACTIONr_mcangle_other4.4986.5151583
X-RAY DIFFRACTIONr_scbond_it3.5484.7761454
X-RAY DIFFRACTIONr_scbond_other3.5334.7611451
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6487.0032116
X-RAY DIFFRACTIONr_long_range_B_refined7.64350.0043030
X-RAY DIFFRACTIONr_long_range_B_other7.55749.8562999
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 86 -
Rwork0.281 1591 -
obs--99.94 %

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