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- PDB-6cpf: Structure of dephosphorylated Aurora A (122-403) bound to AMPPCP ... -

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Basic information

Entry
Database: PDB / ID: 6cpf
TitleStructure of dephosphorylated Aurora A (122-403) bound to AMPPCP 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 / 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 / negative regulation of protein binding / 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 / 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 / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsOtten, R. / Zorba, A. / 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
SupersessionJun 27, 2018ID: 4UTD
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

Downloads & links

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Assembly

Deposited unit
A: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5203
Polymers32,9911
Non-polymers5302
Water1086
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)81.750, 81.750, 172.871
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-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Crystals were obtained by mixing 570 uM Aurora A (18 mg/mL) in buffer (20 mM Tris-HCl, pH 7.5, 200 mM NaCl, 20 mM MgCl2, 1 mM TCEP) in a 2:1 ratio with mother liquor (0.2 M Tris-HCl, pH 7.5, ...Details: Crystals were obtained by mixing 570 uM Aurora A (18 mg/mL) in buffer (20 mM Tris-HCl, pH 7.5, 200 mM NaCl, 20 mM MgCl2, 1 mM TCEP) in a 2:1 ratio with mother liquor (0.2 M Tris-HCl, pH 7.5, 0.2 M ammonium sulfate, 30% (w/v) PEG-3350).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999941 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2012
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999941 Å / Relative weight: 1
ReflectionResolution: 2.3→86.44 Å / Num. all: 154145 / Num. obs: 15873 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 55.9 Å2 / Net I/σ(I): 10.3
Reflection shellResolution: 2.3→2.39 Å / Num. unique all: 1613

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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: 2.3→54.79 Å / SU ML: 0.3526 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2215
RfactorNum. reflection% reflection
Rfree0.2587 1575 10.05 %
Rwork0.2179 --
obs0.2221 15756 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 69.63 Å2
Refinement stepCycle: LAST / Resolution: 2.3→54.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 32 6 2093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032142
X-RAY DIFFRACTIONf_angle_d0.54142916
X-RAY DIFFRACTIONf_chiral_restr0.0394318
X-RAY DIFFRACTIONf_plane_restr0.0037368
X-RAY DIFFRACTIONf_dihedral_angle_d8.90961256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.4021450.32861286X-RAY DIFFRACTION99.93
2.34-2.390.37291430.32661276X-RAY DIFFRACTION100
2.39-2.430.32381400.30421282X-RAY DIFFRACTION100
2.43-2.480.3451500.29251304X-RAY DIFFRACTION99.93
2.48-2.540.32771360.27871273X-RAY DIFFRACTION100
2.54-2.60.31361430.27231259X-RAY DIFFRACTION100
2.6-2.660.34111480.25441300X-RAY DIFFRACTION100
2.66-2.730.30431480.24891295X-RAY DIFFRACTION99.93
2.73-2.810.28281390.25461277X-RAY DIFFRACTION100
2.81-2.90.28571440.25141280X-RAY DIFFRACTION100
2.9-3.010.33091400.24861295X-RAY DIFFRACTION100
3.01-3.130.31961450.24061278X-RAY DIFFRACTION99.93
3.13-3.270.29141380.22991297X-RAY DIFFRACTION99.93
3.27-3.440.23811410.21811280X-RAY DIFFRACTION99.93
3.44-3.660.24051430.2291274X-RAY DIFFRACTION99.72
3.66-3.940.24021410.21611211X-RAY DIFFRACTION94.68
3.94-4.340.20891450.16821296X-RAY DIFFRACTION100
4.34-4.960.20781410.17641266X-RAY DIFFRACTION99.36
4.96-6.250.26151470.21311285X-RAY DIFFRACTION99.72
6.25-54.790.25481440.19931284X-RAY DIFFRACTION99.58

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