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- PDB-5ory: Crystal structure of Aurora-A kinase in complex with an allosteri... -

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Basic information

Entry
Database: PDB / ID: 5ory
TitleCrystal structure of Aurora-A kinase in complex with an allosterically binding fragment
ComponentsAurora kinase A
KeywordsTRANSFERASE / kinase / allosteric inhibitor / fragment
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 / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of mitotic nuclear division / 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 / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / regulation of protein stability / mitotic spindle / 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 / 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
ADENOSINE-5'-DIPHOSPHATE / 2,4-bis(fluoranyl)-6-(1~{H}-pyrazol-3-yl)phenol / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.99 Å
AuthorsMcIntyre, P.J. / Collins, P.M. / von Delft, F. / Bayliss, R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC24461/A12772 United Kingdom
Cancer Research UKC24461/A23302 United Kingdom
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Characterization of Three Druggable Hot-Spots in the Aurora-A/TPX2 Interaction Using Biochemical, Biophysical, and Fragment-Based Approaches.
Authors: McIntyre, P.J. / Collins, P.M. / Vrzal, L. / Birchall, K. / Arnold, L.H. / Mpamhanga, C. / Coombs, P.J. / Burgess, S.G. / Richards, M.W. / Winter, A. / Veverka, V. / Delft, F.V. / Merritt, A. / Bayliss, R.
History
DepositionAug 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name

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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)31,5778
Polymers30,7981
Non-polymers7787
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-55 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.140, 82.140, 176.250
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-404-

CL

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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 / hARK1 / Breast tumor-amplified kinase / Serine/threonine- ...Aurora 2 / Aurora/IPL1-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: 30798.236 Da / Num. of mol.: 1
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
Production host: Escherichia coli (E. coli)
References: UniProt: O14965, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 67 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-AY4 / 2,4-bis(fluoranyl)-6-(1~{H}-pyrazol-3-yl)phenol


Mass: 196.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6F2N2O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5: 0.5 M NaCl: 0.2 M MgCl2: 32.5 % v/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.99→71.135 Å / Num. obs: 45709 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.271 % / Biso Wilson estimate: 58.34 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.047 / Χ2: 1.038 / Net I/σ(I): 23.36 / Num. measured all: 469458 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.99-2.0410.3922.0611.1133820.482.168100
2.04-2.110.2111.3421.7232910.6651.41399.9
2.1-2.169.3650.8592.6732190.8180.91100
2.16-2.2210.5780.6373.7731090.9060.669100
2.22-2.310.820.4345.5230070.9510.45599.9
2.3-2.3810.7770.3227.4228990.9750.338100
2.38-2.4710.720.259.4928130.9840.263100
2.47-2.5710.6220.18412.6927330.9910.194100
2.57-2.6810.4070.13716.6825890.9950.14499.9
2.68-2.819.4220.121.1824600.9970.106100
2.81-2.9710.9060.07330.7823670.9990.077100
2.97-3.1510.8380.0637.3522520.9990.063100
3.15-3.3610.5030.04746.5320770.9990.049100
3.36-3.6310.0850.03953.4319610.9990.04199.9
3.63-3.989.1690.03456.9218010.9990.036100
3.98-4.459.2950.0363.17162210.03199.8
4.45-5.1410.2670.02768.26145110.028100
5.14-6.2910.0360.02866.25120810.03100
6.29-8.99.1670.02566.2393810.026100
8.9-71.13510.5110.02273.0653010.02399.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
xia2data reduction
PHENIXphasing
RefinementResolution: 1.99→71.135 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.95
RfactorNum. reflection% reflection
Rfree0.2654 1253 5.02 %
Rwork0.2043 --
obs0.2072 24936 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 247.4 Å2 / Biso mean: 61.3357 Å2 / Biso min: 34.03 Å2
Refinement stepCycle: final / Resolution: 1.99→71.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2137 0 46 60 2243
Biso mean--73.54 58.37 -
Num. residues----265
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)
14.53072.80490.68183.8519-0.270.7555-0.180.0725-0.5903-0.39720.2682-0.52660.59630.0529-0.07950.5302-0.09110.04470.4986-0.15850.5158-0.880222.2815-12.1242
27.35622.097-1.6263.939-3.86973.97510.0390.4443-0.8811-0.6141-0.12320.4153-0.1377-1.36820.10070.6691-0.0378-0.04370.5831-0.21320.5348-16.718420.4421-16.6871
33.8382-1.2026-0.49684.05031.23351.667-0.07630.1163-0.0197-0.30780.16550.0672-0.0737-0.0829-0.11630.4294-0.045-0.05970.4691-0.0190.3606-15.046133.2407-11.0039
44.33182.06741.9893.56631.50585.7410.14720.2924-0.2801-0.0455-0.10970.09830.3842-0.408-0.09480.39480.0206-0.06180.4163-0.05890.5037-28.23532.3895-3.5092
56.16950.83730.62584.7599-2.96694.4746-0.267-1.0305-0.1460.9181-0.10.50190.3799-0.59450.39130.5498-0.01710.14830.4535-0.09160.5003-28.847130.33967.7887
64.5541.3269-0.59735.6502-0.36024.45910.01710.00780.81880.29540.02910.5805-0.6551-0.3161-0.0330.3790.1057-0.04590.3801-0.11570.6782-31.56345.30713.132
72.77331.251-0.08825.0580.07594.2506-0.0220.32520.7873-0.4496-0.00560.458-0.6328-0.5475-0.05280.49090.104-0.12640.51630.06170.6461-29.707945.6685-9.9113
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 127 through 172 )A127 - 172
2X-RAY DIFFRACTION2chain 'A' and (resid 173 through 187 )A173 - 187
3X-RAY DIFFRACTION3chain 'A' and (resid 188 through 287 )A188 - 287
4X-RAY DIFFRACTION4chain 'A' and (resid 289 through 324 )A289 - 324
5X-RAY DIFFRACTION5chain 'A' and (resid 325 through 342 )A325 - 342
6X-RAY DIFFRACTION6chain 'A' and (resid 343 through 363 )A343 - 363
7X-RAY DIFFRACTION7chain 'A' and (resid 364 through 391 )A364 - 391

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