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- PDB-8of5: Crystal structure of Aurora A 122-403 C290A, N332A, Q335A, C393A ... -

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Basic information

Entry
Database: PDB / ID: 8of5
TitleCrystal structure of Aurora A 122-403 C290A, N332A, Q335A, C393A bound to ADP
ComponentsAurora kinase A
KeywordsTRANSFERASE / Kinase / Autophosphorylation / Redox
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 / positive regulation of oocyte maturation / spindle pole centrosome / 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 / positive regulation of oocyte maturation / spindle pole centrosome / 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 / spindle organization / positive regulation of mitochondrial fission / 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 / positive regulation of mitotic nuclear division / AURKA Activation by TPX2 / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / mitotic spindle organization / ciliary basal body / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / negative regulation of protein binding / 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 microtubule / mitotic spindle / kinetochore / response to wounding / spindle / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / basolateral plasma membrane / peptidyl-serine phosphorylation / proteasome-mediated ubiquitin-dependent protein catabolic process / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / postsynaptic density / 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 / 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
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / NITRATE ION / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsMiles, J.A. / Hammond, K.L.R. / Bayliss, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V003577/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of Aurora A 122-403 C290A, N332A, Q335A, C393A bound to ADP
Authors: Miles, J.A. / Hammond, K.L.R. / Bayliss, R.
History
DepositionMar 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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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)33,97810
Polymers32,7851
Non-polymers1,1949
Water2,504139
1
A: Aurora kinase A
hetero molecules

A: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,95720
Polymers65,5692
Non-polymers2,38818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area9570 Å2
ΔGint-75 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.490, 83.490, 116.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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 / Breast tumor-amplified ...Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / Breast tumor-amplified kinase / Ipl1- and aurora-related kinase 1 / Serine/threonine-protein kinase 15 / Serine/threonine-protein kinase 6 / Serine/threonine-protein kinase Ayk1 / Serine/threonine-protein kinase aurora-A


Mass: 32784.582 Da / Num. of mol.: 1 / Mutation: C290A C393A N332A Q335A
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 , 7 types, 148 molecules

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


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: PEG 1000, PEG 3350, MPD, MOPS, Hepes, Magnesium chloride, Calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.97→47.791 Å / Num. obs: 29889 / % possible obs: 100 % / Redundancy: 14.1 % / CC1/2: 1 / Net I/σ(I): 20.3
Reflection shellResolution: 1.97→2.021 Å / Num. unique obs: 2058 / CC1/2: 0.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→47.791 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.249 / WRfactor Rwork: 0.191 / SU B: 9.234 / SU ML: 0.122 / Average fsc free: 0.9471 / Average fsc work: 0.9565 / Cross valid method: FREE R-VALUE / ESU R: 0.13 / ESU R Free: 0.136
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2354 1501 5.033 %
Rwork0.1837 28324 -
all0.186 --
obs-29825 99.983 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 61.375 Å2
Baniso -1Baniso -2Baniso -3
1--1.853 Å20 Å20 Å2
2---1.853 Å2-0 Å2
3---3.706 Å2
Refinement stepCycle: LAST / Resolution: 1.97→47.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2151 0 74 139 2364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122276
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162149
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.6643083
X-RAY DIFFRACTIONr_angle_other_deg0.4771.5714946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4325264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.419521
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.41351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00810380
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.4110105
X-RAY DIFFRACTIONr_chiral_restr0.070.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022600
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02537
X-RAY DIFFRACTIONr_nbd_refined0.2050.2443
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.21852
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21074
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21168
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2119
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2210.230
X-RAY DIFFRACTIONr_nbd_other0.1680.2125
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.216
X-RAY DIFFRACTIONr_mcbond_it3.4784.5671059
X-RAY DIFFRACTIONr_mcbond_other3.4514.5681059
X-RAY DIFFRACTIONr_mcangle_it4.2528.1821322
X-RAY DIFFRACTIONr_mcangle_other4.2558.1851323
X-RAY DIFFRACTIONr_scbond_it5.6075.2211217
X-RAY DIFFRACTIONr_scbond_other5.6035.2161215
X-RAY DIFFRACTIONr_scangle_it7.9629.3161761
X-RAY DIFFRACTIONr_scangle_other7.9599.3121759
X-RAY DIFFRACTIONr_lrange_it9.57858.3799401
X-RAY DIFFRACTIONr_lrange_other9.57157.8879317
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.97-2.0210.351940.37120580.3721520.8570.861000.372
2.021-2.0760.3311040.33220270.33221310.8850.8911000.327
2.076-2.1360.3191130.29919180.30120310.9140.9191000.285
2.136-2.2020.2571000.25218970.25219980.9540.94999.950.23
2.202-2.2740.2391170.23418140.23519310.9560.9581000.208
2.274-2.3540.2491080.217490.20218570.9480.9711000.17
2.354-2.4420.243790.20917520.21118310.9530.9691000.182
2.442-2.5420.226760.17416560.17617320.9670.9811000.147
2.542-2.6550.27900.18116010.18616910.9620.9811000.154
2.655-2.7840.21670.18115500.18216170.9760.9831000.158
2.784-2.9340.253680.19814670.20115350.9590.9761000.179
2.934-3.1110.245780.18513890.18814670.9660.981000.172
3.111-3.3250.258750.1912980.19313730.9530.9761000.184
3.325-3.590.222720.18412210.18612930.9720.9791000.189
3.59-3.930.187550.15311310.15411860.9820.9871000.163
3.93-4.390.194560.14310400.14610960.9780.9881000.166
4.39-5.0620.204510.159220.1539730.9770.9871000.182
5.062-6.1830.269430.1937940.1978370.9610.9791000.236
6.183-8.6710.255280.1946430.1966720.9530.97799.85120.251
8.671-47.7910.257270.1933970.1984240.9850.9741000.24
Refinement TLS params.Method: refined / Origin x: -6.203 Å / Origin y: -16.8685 Å / Origin z: -24.4766 Å
111213212223313233
T0.0908 Å20.0048 Å20.0439 Å2-0.1268 Å20.0444 Å2--0.0414 Å2
L1.8079 °20.0095 °2-0.1917 °2-1.9412 °2-0.5679 °2--1.2158 °2
S-0.0153 Å °0.0103 Å °0.0659 Å °-0.1464 Å °0.0444 Å °0.0174 Å °0.0126 Å °-0.0781 Å °-0.0291 Å °
Refinement TLS groupSelection: ALL

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