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- PDB-4c3r: Structure of dephosphorylated Aurora A (122-403) bound to AMPPCP -

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Basic information

Entry
Database: PDB / ID: 4c3r
TitleStructure of dephosphorylated Aurora A (122-403) bound to AMPPCP
ComponentsAURORA KINASE A
KeywordsTRANSFERASE / AURORA A / ACTIVATION / CELL CYCLE / CANCER
Function / homology
Function and homology information


Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / cilium disassembly / spindle pole centrosome / mitotic centrosome separation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / regulation of G2/M transition of mitotic cell cycle ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / cilium disassembly / spindle pole centrosome / mitotic centrosome separation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / regulation of G2/M transition of mitotic cell cycle / germinal vesicle / meiotic spindle organization / meiotic spindle / spindle organization / positive regulation of mitochondrial fission / mitotic spindle pole / spindle midzone / SUMOylation of DNA replication proteins / negative regulation of protein binding / positive regulation of mitotic cell cycle / positive regulation of mitotic nuclear division / protein serine/threonine/tyrosine kinase activity / centriole / liver regeneration / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / AURKA Activation by TPX2 / regulation of signal transduction by p53 class mediator / molecular function activator activity / mitotic spindle organization / regulation of cytokinesis / G2/M transition of mitotic cell cycle / response to wounding / regulation of protein stability / peptidyl-serine phosphorylation / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / spindle / kinetochore / spindle pole / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / protein autophosphorylation / mitotic cell cycle / ciliary basal body / midbody / Regulation of TP53 Activity through Phosphorylation / basolateral plasma membrane / microtubule / protein kinase activity / protein phosphorylation / non-specific serine/threonine protein kinase / postsynaptic density / protein heterodimerization activity / negative regulation of gene expression / protein serine kinase activity / cell division / ubiquitin protein ligase binding / protein serine/threonine kinase activity / centrosome / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Aurora kinase A / Aurora kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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: 2.79 Å
AuthorsZorba, A. / Kutter, S. / Cho, Y.-J. / Kern, D.
CitationJournal: Elife / Year: 2014
Title: Molecular Mechanism of Aurora a Kinase Autophosphorylation and its Allosteric Activation by Tpx2.
Authors: Zorba, A. / Buosi, V. / Kutter, S. / Kern, N. / Pontiggia, F. / Cho, Y.J. / Kern, D.
History
DepositionAug 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)33,1952
Polymers32,6891
Non-polymers5051
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.468, 83.468, 172.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein AURORA KINASE A / AURORA 2 / AURORA/IPL1-RELATED KINASE 1 / ARK-1 / AURORA-RELAT ED KINASE 1 / HARK1 / BREAST TUMOR- ...AURORA 2 / AURORA/IPL1-RELATED KINASE 1 / ARK-1 / AURORA-RELAT ED KINASE 1 / HARK1 / BREAST TUMOR-AMPLIFIED KINASE / SERINE/THREONIN E-PROTEIN KINASE 15 / SERINE/THREONINE-PROTEIN KINASE 6 / SERINE/THR EONINE-PROTEIN KINASE AURORA-A / AURORA A KINASE


Mass: 32689.459 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 122-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / 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 / Comment: AMP-PCP, energy-carrying molecule analogue*YM

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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: 2.96 Å3/Da / Density % sol: 58.54 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: CRYSTALS OF DEPHOSPHORYLATED A(122-403) IN COMPLEX WITH AMPPCP WERE OBTAINED BY MIXING A 2:1 RATIO OF 570UM (18MG/ML) DEP A(122-403) AND 1MM AMPPCP WITH MOTHER LIQUOR (0.2M AMMONIUM SULFATE, ...Details: CRYSTALS OF DEPHOSPHORYLATED A(122-403) IN COMPLEX WITH AMPPCP WERE OBTAINED BY MIXING A 2:1 RATIO OF 570UM (18MG/ML) DEP A(122-403) AND 1MM AMPPCP WITH MOTHER LIQUOR (0.2M AMMONIUM SULFATE, 0.2M TRISHCL PH 7.50, 30% (W/V) PEG3350). THE CRYSTALS WERE GROWN AT 18C BY VAPOR DIFFUSION AND THE HANGING DROP METHOD.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999941
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 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: 2.79→55.4 Å / Num. obs: 9400 / % possible obs: 100 % / Observed criterion σ(I): 1.8 / Redundancy: 15.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.8
Reflection shellResolution: 2.79→2.87 Å / Redundancy: 16.7 % / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OL7

1ol7


Resolution: 2.79→55.42 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.901 / SU B: 16.737 / SU ML: 0.332 / Cross valid method: THROUGHOUT / ESU R: 4.704 / ESU R Free: 0.442 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.30601 941 10 %RANDOM
Rwork0.22124 ---
obs0.22939 8459 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.433 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.03 Å20 Å2
2---0.03 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.79→55.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 31 0 2105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192159
X-RAY DIFFRACTIONr_bond_other_d0.0020.022061
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.9822925
X-RAY DIFFRACTIONr_angle_other_deg0.83434737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4965250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54422.952105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.54415378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9531518
X-RAY DIFFRACTIONr_chiral_restr0.0790.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212373
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02520
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.794→2.866 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.451 81 -
Rwork0.327 588 -
obs--100 %

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