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- PDB-4jbq: Novel Aurora kinase inhibitors reveal mechanisms of HURP in nucle... -

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Basic information

Entry
Database: PDB / ID: 4jbq
TitleNovel Aurora kinase inhibitors reveal mechanisms of HURP in nucleation of centrosomal and kinetochore microtubules
ComponentsAurora Kinase A
KeywordsTRANSFERASE / Aurora Kinase inhibitors / HURP / mitotic spindle
Function / homology
Function and homology information


Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / meiotic spindle / mitotic centrosome separation / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / positive regulation of mitochondrial fission / spindle organization / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / centriole / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic cell cycle / AURKA Activation by TPX2 / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of mitotic nuclear division / mitotic spindle organization / ciliary basal body / negative regulation of protein binding / regulation of signal transduction by p53 class mediator / regulation of cytokinesis / molecular function activator activity / liver regeneration / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / regulation of protein stability / spindle / mitotic spindle / kinetochore / response to wounding / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / proteasome-mediated ubiquitin-dependent protein catabolic process / basolateral plasma membrane / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / microtubule / postsynaptic density / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / cell division / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Aurora kinase A / 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 ...Aurora kinase A / 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 / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsWu, J.S. / Leou, J.S. / Peng, Y.H. / Hsueh, C.C. / Hsieh, H.P. / Wu, S.Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Aurora kinase inhibitors reveal mechanisms of HURP in nucleation of centrosomal and kinetochore microtubules.
Authors: Wu, J.M. / Chen, C.T. / Coumar, M.S. / Lin, W.H. / Chen, Z.J. / Hsu, J.T. / Peng, Y.H. / Shiao, H.Y. / Lin, W.H. / Chu, C.Y. / Wu, J.S. / Lin, C.T. / Chen, C.P. / Hsueh, C.C. / Chang, K.Y. / ...Authors: Wu, J.M. / Chen, C.T. / Coumar, M.S. / Lin, W.H. / Chen, Z.J. / Hsu, J.T. / Peng, Y.H. / Shiao, H.Y. / Lin, W.H. / Chu, C.Y. / Wu, J.S. / Lin, C.T. / Chen, C.P. / Hsueh, C.C. / Chang, K.Y. / Kao, L.P. / Huang, C.Y. / Chao, Y.S. / Wu, S.Y. / Hsieh, H.P. / Chi, Y.H.
History
DepositionFeb 20, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Aurora Kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8242
Polymers32,3591
Non-polymers4651
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.414, 82.414, 170.349
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Aurora Kinase A / / Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / hARK1 / Breast tumor- ...Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / hARK1 / Breast tumor-amplified kinase / Serine/threonine-protein kinase 15 / Serine/threonine-protein kinase 6 / Serine/threonine-protein kinase aurora-A


Mass: 32359.123 Da / Num. of mol.: 1 / Fragment: Catalytic domain, UNP RESIDUES 123-401 / Mutation: T288D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6
Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-VX6 / CYCLOPROPANECARBOXYLIC ACID {4-[4-(4-METHYL-PIPERAZIN-1-YL)-6-(5-METHYL-2H-PYRAZOL-3-YLAMINO)-PYRIMIDIN-2-YLSULFANYL]-PHENYL}-AMIDE / Tozasertib


Mass: 464.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28N8OS / Comment: inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.58 Å3/Da / Density % sol: 52.33 % / Mosaicity: 0.674 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG 400, 0.1M ammonia sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 15940 / % possible obs: 99.8 % / Redundancy: 17.1 % / Rmerge(I) obs: 0.059 / Χ2: 1.06 / Net I/σ(I): 17.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3817.70.4815291.0681100
2.38-2.4817.80.38415591.0691100
2.48-2.5917.80.26215571.0771100
2.59-2.7317.70.18815581.081100
2.73-2.917.70.12715581.0181100
2.9-3.1217.50.09115831.0461100
3.12-3.4317.30.06715991.041100
3.43-3.9316.80.0516001.0691100
3.93-4.9516.10.0416361.072199.9
4.95-3014.60.03617611.063198.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.135 / WRfactor Rwork: 0.1049 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.9374 / SU B: 13.95 / SU ML: 0.171 / SU R Cruickshank DPI: 0.1322 / SU Rfree: 0.1099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2823 794 5 %RANDOM
Rwork0.2244 ---
obs0.2272 15882 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.23 Å2 / Biso mean: 54.4488 Å2 / Biso min: 28.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å2-0.83 Å20 Å2
2---1.67 Å20 Å2
3---2.5 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2113 0 33 21 2167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022203
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.9822978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1975255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34122.83106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54115387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4881519
X-RAY DIFFRACTIONr_chiral_restr0.0710.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211676
LS refinement shellResolution: 2.299→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 47 -
Rwork0.232 932 -
all-979 -
obs--99.09 %
Refinement TLS params.Method: refined / Origin x: 16.383 Å / Origin y: 32.347 Å / Origin z: 7.824 Å
111213212223313233
T0.1238 Å20.046 Å2-0.0183 Å2-0.1481 Å2-0.0231 Å2--0.0797 Å2
L4.4137 °20.9332 °2-1.7934 °2-2.0976 °2-0.8895 °2--1.5389 °2
S-0.1137 Å °-0.4314 Å °-0.2131 Å °-0.0165 Å °0.0488 Å °-0.0793 Å °0.0809 Å °0.1965 Å °0.065 Å °

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