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- PDB-4j8m: Aurora A in complex with CD532 -

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Basic information

Entry
Database: PDB / ID: 4j8m
TitleAurora A in complex with CD532
ComponentsAurora kinase A
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Aurora A / type II / kinase inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / mitotic spindle organization / positive regulation of mitotic nuclear division / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / ciliary basal body / negative regulation of protein binding / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / molecular function activator activity / liver regeneration / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / regulation of protein stability / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / mitotic spindle / kinetochore / spindle / 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 / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / 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-CJ5 / PHOSPHATE ION / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.853 Å
AuthorsMeyerowitz, J.G. / Gustafson, W.C. / Shokat, K.M. / Weiss, W.A.
CitationJournal: Cancer Cell / Year: 2014
Title: Drugging MYCN through an Allosteric Transition in Aurora Kinase A.
Authors: Gustafson, W.C. / Meyerowitz, J.G. / Nekritz, E.A. / Chen, J. / Benes, C. / Charron, E. / Simonds, E.F. / Seeger, R. / Matthay, K.K. / Hertz, N.T. / Eilers, M. / Shokat, K.M. / Weiss, W.A.
History
DepositionFeb 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software

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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)33,3397
Polymers32,4791
Non-polymers8606
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.175, 92.943, 74.542
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-605-

HOH

21A-761-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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: 32479.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: AIK, AIRK1, ARK1, AURA, AURKA, AYK1, BTAK, IAK1, STK15, STK6
Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O14965, non-specific serine/threonine protein kinase

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Non-polymers , 6 types, 178 molecules

#2: Chemical ChemComp-CJ5 / 1-[4-[[4-[(5-cyclopentyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl]amino]phenyl]-3-[3-(trifluoromethyl)phenyl]urea


Mass: 522.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H25F3N8O
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20 mg/ml Aurora A protein, 1 mM CD532, 20% (w/v) PEG8000, 0.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate trihydrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0088 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2012
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0088 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 24605 / Num. obs: 24605 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.85-1.886.60.791198.3
1.88-1.926.60.656197.8
1.92-1.956.60.502198.2
1.95-1.996.70.436198.7
1.99-2.046.60.351198.4
2.04-2.086.60.302198.4
2.08-2.146.60.255198.5
2.14-2.196.60.22198.5
2.19-2.266.60.196198.7
2.26-2.336.60.173199
2.33-2.416.60.154199.1
2.41-2.516.60.143199.3
2.51-2.626.60.13199.4
2.62-2.766.50.125199
2.76-2.946.50.108199.7
2.94-3.166.40.103199.5
3.16-3.486.40.104199.7
3.48-3.986.30.085199.7
3.98-5.0160.084199.5
5.01-306.10.069199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.4 Å29.08 Å
Translation2.4 Å29.08 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.4.0phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.853→29.075 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.18 / σ(F): 1.42 / Phase error: 20.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.218 1982 8.15 %
Rwork0.1747 --
obs0.1782 24311 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.2172 Å2
Refinement stepCycle: LAST / Resolution: 1.853→29.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2189 0 56 172 2417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082299
X-RAY DIFFRACTIONf_angle_d1.1323107
X-RAY DIFFRACTIONf_dihedral_angle_d18.746879
X-RAY DIFFRACTIONf_chiral_restr0.062325
X-RAY DIFFRACTIONf_plane_restr0.006393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8533-1.89960.27871300.22561459X-RAY DIFFRACTION90
1.8996-1.9510.27641380.21521540X-RAY DIFFRACTION96
1.951-2.00840.27161350.20421530X-RAY DIFFRACTION96
2.0084-2.07320.21911410.18961587X-RAY DIFFRACTION97
2.0732-2.14730.24351420.1781585X-RAY DIFFRACTION98
2.1473-2.23320.20791390.17341553X-RAY DIFFRACTION98
2.2332-2.33480.22681410.17671593X-RAY DIFFRACTION98
2.3348-2.45780.22361430.16371593X-RAY DIFFRACTION99
2.4578-2.61170.22961420.17431619X-RAY DIFFRACTION99
2.6117-2.81320.19071410.18151597X-RAY DIFFRACTION99
2.8132-3.09610.24771460.18141652X-RAY DIFFRACTION99
3.0961-3.54340.25171430.1821616X-RAY DIFFRACTION99
3.5434-4.46170.20081480.15381673X-RAY DIFFRACTION100
4.4617-29.07870.17911530.17141732X-RAY DIFFRACTION100
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)
17.31360.8622.09865.3905-0.27478.41250.08770.183-0.1651-0.2817-0.0445-0.12950.01450.1326-0.03850.12620.02520.04190.1923-0.02830.1618125.8367112.8405153.8498
23.8439-0.05780.80563.22781.51397.27520.07080.65240.2391-0.5578-0.12070.3396-0.0596-0.15580.10360.3212-0.0055-0.06020.21590.05970.2366116.0094115.4024149.7595
32.3161.3329-0.85022.8144-1.81982.2230.0029-0.114-0.0402-0.0314-0.1099-0.0350.00190.0850.11510.14150.0138-0.02840.1929-0.03980.1551111.4772108.4151164.0268
46.60620.1972.47145.3925-0.9927.7894-0.00150.3624-0.4519-0.690.18170.21640.49610.0334-0.1240.2323-0.0358-0.0120.26970.00570.2644109.1949103.2604158.3846
57.3707-2.71013.87034.0612-1.96046.7565-0.0725-0.1845-0.2782-0.2652-0.16220.595-0.749-1.09170.21250.42740.1302-0.05040.4187-0.11570.464794.07797.7316153.7189
62.2719-0.1492-0.00821.2496-0.68386.654-0.040.0709-0.3442-0.0598-0.02490.14940.672-0.09560.08490.1608-0.00220.04160.213-0.02580.319797.896190.6941162.8032
74.9806-0.28761.83883.53410.18644.7974-0.1114-0.2435-0.08870.3638-0.12790.72210.0098-0.37130.21030.18590.0040.12180.2912-0.01330.333192.6106100.7396172.203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 127 through 152 )
2X-RAY DIFFRACTION2chain 'A' and (resid 153 through 187 )
3X-RAY DIFFRACTION3chain 'A' and (resid 188 through 250 )
4X-RAY DIFFRACTION4chain 'A' and (resid 251 through 292 )
5X-RAY DIFFRACTION5chain 'A' and (resid 293 through 307 )
6X-RAY DIFFRACTION6chain 'A' and (resid 308 through 353 )
7X-RAY DIFFRACTION7chain 'A' and (resid 354 through 389 )

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