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- PDB-6gr8: Human AURKC INCENP complex bound to BRD-7880 -

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Basic information

Entry
Database: PDB / ID: 6gr8
TitleHuman AURKC INCENP complex bound to BRD-7880
Components
  • Aurora kinase C
  • Inner centromere protein
KeywordsTRANSFERASE / Kinase / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


central element / meiotic spindle midzone / meiotic spindle midzone assembly / 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 ...central element / meiotic spindle midzone / meiotic spindle midzone assembly / 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 / chromosome passenger complex / positive regulation of cytokinesis / mitotic cytokinesis / SUMOylation of DNA replication proteins / chromosome, centromeric region / mitotic spindle assembly / spindle midzone / pericentric heterochromatin / condensed chromosome / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / protein serine/threonine/tyrosine kinase activity / Resolution of Sister Chromatid Cohesion / molecular function activator activity / regulation of cytokinesis / mitotic spindle organization / meiotic cell cycle / spindle microtubule / chromosome segregation / RHO GTPases Activate Formins / kinetochore / spindle / spindle pole / Separation of Sister Chromatids / mitotic cell cycle / microtubule cytoskeleton / midbody / microtubule / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / nuclear body / protein phosphorylation / cell division / protein serine kinase activity / centrosome / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-F8Z / Inner centromere protein / Aurora kinase C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 23, 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)41,0603
Polymers40,4702
Non-polymers5911
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-33 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.650, 72.480, 83.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Production host: Escherichia coli BL21(DE3) (bacteria)
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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NQS7
#3: Chemical ChemComp-F8Z / 1-[(2~{R},3~{S})-2-[[1,3-benzodioxol-5-ylmethyl(methyl)amino]methyl]-3-methyl-6-oxidanylidene-5-[(2~{S})-1-oxidanylpropan-2-yl]-3,4-dihydro-2~{H}-1,5-benzoxazocin-8-yl]-3-(4-methoxyphenyl)urea


Mass: 590.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H38N4O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium chloride, 25% PEG3350, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Dec 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.75→56.65 Å / Num. obs: 34077 / % possible obs: 97.1 % / Redundancy: 5.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.8
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1433 / CC1/2: 0.709 / % possible all: 77.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AF3

4af3


Resolution: 1.75→54.61 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.063 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.122 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21626 1712 5 %RANDOM
Rwork0.17648 ---
obs0.1785 32319 96.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.932 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å2-0 Å20 Å2
2--2.91 Å2-0 Å2
3----0.86 Å2
Refinement stepCycle: 1 / Resolution: 1.75→54.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 43 311 3122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0142942
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172663
X-RAY DIFFRACTIONr_angle_refined_deg1.351.6754014
X-RAY DIFFRACTIONr_angle_other_deg0.8941.6266256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6145352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76520.247162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11215502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8391527
X-RAY DIFFRACTIONr_chiral_restr0.2190.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023249
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02535
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_it1.3971.8141366
X-RAY DIFFRACTIONr_mcbond_other1.3911.8121365
X-RAY DIFFRACTIONr_mcangle_it2.2722.7091708
X-RAY DIFFRACTIONr_mcangle_other2.2752.7111709
X-RAY DIFFRACTIONr_scbond_it1.8442.0081576
X-RAY DIFFRACTIONr_scbond_other1.8432.0081577
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0042.9362299
X-RAY DIFFRACTIONr_long_range_B_refined5.28721.7653434
X-RAY DIFFRACTIONr_long_range_B_other5.28621.7613435
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 89 -
Rwork0.304 1907 -
obs--77.94 %

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