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- PDB-6cpe: Structure of apo, dephosphorylated Aurora A (122-403) in an activ... -

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Basic information

Entry
Database: PDB / ID: 6cpe
TitleStructure of apo, dephosphorylated Aurora A (122-403) in an active conformation
ComponentsAurora kinase A
KeywordsTRANSFERASE / protein kinase / DFG-loop / cell cycle
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
1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsOtten, R. / Kutter, S. / Buosi, V. / Padua, R.A.P. / Kern, D.
Funding support United States, 4items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Office of Basic Energy Sciences, Catalysis Science Program United States
Department of Energy (DOE, United States)DE-FG02-05ER15699 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100966-01 United States
CitationJournal: Elife / Year: 2018
Title: Dynamics of human protein kinase Aurora A linked to drug selectivity.
Authors: Pitsawong, W. / Buosi, V. / Otten, R. / Agafonov, R.V. / Zorba, A. / Kern, N. / Kutter, S. / Kern, G. / Padua, R.A. / Meniche, X. / Kern, D.
History
DepositionMar 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1532
Polymers32,9911
Non-polymers1621
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.550, 80.550, 169.790
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#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: 32990.754 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
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-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Diethylene glycol diethyl ether


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: A 1:1 ratio protein:mother liquor was obtained by mixing 0.5 uL Aurora A (300 uM; 10 mg/mL) in 50 mM HEPES, pH 7.3, 500 mM ammonium acetate, 1 mM MgCl2, 5 mM TCEP) with 0.5 uL of 0.15 M Tris- ...Details: A 1:1 ratio protein:mother liquor was obtained by mixing 0.5 uL Aurora A (300 uM; 10 mg/mL) in 50 mM HEPES, pH 7.3, 500 mM ammonium acetate, 1 mM MgCl2, 5 mM TCEP) with 0.5 uL of 0.15 M Tris-HCl, pH 7.5, 0.15 M ammonium sulfate, 35% (w/v) PEG-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00001 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2014
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.45→84.9 Å / Num. all: 96165 / Num. obs: 12688 / % possible obs: 99.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 64.11 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 15
Reflection shellResolution: 2.45→2.55 Å / Rmerge(I) obs: 1.202 / Num. unique all: 1381 / Num. unique obs: 8694

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.13_2998refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MQ4

1mq4


Resolution: 2.45→64.52 Å / SU ML: 0.3634 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.1466
RfactorNum. reflection% reflection
Rfree0.2536 1262 10.12 %
Rwork0.2142 --
obs0.2183 12617 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 78.56 Å2
Refinement stepCycle: LAST / Resolution: 2.45→64.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 11 4 2042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00392098
X-RAY DIFFRACTIONf_angle_d0.60172846
X-RAY DIFFRACTIONf_chiral_restr0.0409314
X-RAY DIFFRACTIONf_plane_restr0.0041362
X-RAY DIFFRACTIONf_dihedral_angle_d9.82631248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.50.38411420.32611256X-RAY DIFFRACTION99.29
2.5-2.560.32761380.31257X-RAY DIFFRACTION99.86
2.56-2.630.37921420.32141278X-RAY DIFFRACTION99.86
2.63-2.70.33341470.31091286X-RAY DIFFRACTION99.86
2.7-2.780.34181410.27291266X-RAY DIFFRACTION99.65
2.78-2.870.2971410.2671280X-RAY DIFFRACTION100
2.87-2.970.34611440.25231274X-RAY DIFFRACTION99.93
2.97-3.090.32721380.25431293X-RAY DIFFRACTION99.93
3.09-3.230.2711430.24421250X-RAY DIFFRACTION99.71
3.23-3.40.31381410.24341266X-RAY DIFFRACTION99.93
3.4-3.610.25751430.23961274X-RAY DIFFRACTION99.93
3.61-3.890.23211500.20271269X-RAY DIFFRACTION99.93
3.89-4.280.19971410.17341272X-RAY DIFFRACTION99.86
4.28-4.90.2151420.15831253X-RAY DIFFRACTION99.43
4.9-6.170.21991420.21681241X-RAY DIFFRACTION96.51
6.17-64.550.24071470.18851257X-RAY DIFFRACTION99.01

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