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- PDB-4c3p: Structure of dephosphorylated Aurora A (122-403) bound to TPX2 an... -

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Basic information

Entry
Database: PDB / ID: 4c3p
TitleStructure of dephosphorylated Aurora A (122-403) bound to TPX2 and AMPPCP
Components
  • AURORA KINASE A
  • TARGETING PROTEIN FOR XKLP2
KeywordsTRANSFERASE / ACTIVATION / ALLOSTERY / CELL CYCLE / CANCER
Function / homology
Function and homology information


importin-alpha family protein binding / Interaction between PHLDA1 and AURKA / activation of protein kinase activity / regulation of centrosome cycle / negative regulation of microtubule depolymerization / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / chromosome passenger complex ...importin-alpha family protein binding / Interaction between PHLDA1 and AURKA / activation of protein kinase activity / regulation of centrosome cycle / negative regulation of microtubule depolymerization / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / chromosome passenger complex / microtubule nucleation / positive regulation of oocyte maturation / pronucleus / mitotic centrosome separation / germinal vesicle / meiotic spindle / 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 / mitotic spindle assembly / spindle midzone / intercellular bridge / regulation of G2/M transition of mitotic cell cycle / negative regulation of protein binding / centriole / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic nuclear division / positive regulation of mitotic cell cycle / regulation of mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / molecular function activator activity / AURKA Activation by TPX2 / liver regeneration / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / mitotic spindle organization / 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 / kinetochore / response to wounding / spindle / spindle pole / G2/M transition of mitotic cell cycle / mitotic spindle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / peptidyl-serine phosphorylation / microtubule cytoskeleton / midbody / protein autophosphorylation / basolateral plasma membrane / molecular adaptor activity / Regulation of TP53 Activity through Phosphorylation / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / postsynaptic density / ciliary basal body / protein phosphorylation / protein heterodimerization activity / cell division / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / centrosome / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / nucleoplasm
Similarity search - Function
TPX2 / Aurora-A binding / TPX2, C-terminal / TPX2 central domain / Targeting protein for Xklp2 (TPX2) domain / Aurora-A binding / Cell cycle regulated microtubule associated protein / Aurora kinase A / Aurora kinase / Phosphorylase Kinase; domain 1 ...TPX2 / Aurora-A binding / TPX2, C-terminal / TPX2 central domain / Targeting protein for Xklp2 (TPX2) domain / Aurora-A binding / Cell cycle regulated microtubule associated protein / 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 / Targeting protein for Xklp2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsZorba, A. / Kutter, S. / 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
B: TARGETING PROTEIN FOR XKLP2
D: AURORA KINASE A
E: TARGETING PROTEIN FOR XKLP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3407
Polymers75,2334
Non-polymers1,1063
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10200 Å2
ΔGint-56.4 kcal/mol
Surface area25930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.927, 86.717, 153.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 2 / Fragment: KINASE DOMAIN, RESIDUES 121-403
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: Protein/peptide TARGETING PROTEIN FOR XKLP2 / DIFFERENTIALLY EXPRESSED IN CANCEROUS AND NON-CANCEROUS LUN G CELLS 2 / DIL-2 / HEPATOCELLULAR ...DIFFERENTIALLY EXPRESSED IN CANCEROUS AND NON-CANCEROUS LUN G CELLS 2 / DIL-2 / HEPATOCELLULAR CARCINOMA-ASSOCIATED ANTIGEN 519 / PROTEIN FLS353 / RESTRICTED EXPRESSION PROLIFERATION-ASSOCIATED PR OTEIN 100 / P100 / TARGETING PROTEIN FOR XKLP2 / TPX2


Mass: 4927.110 Da / Num. of mol.: 2 / Fragment: AURORA A KINASE BINDING DOMAIN, RESIDUES 1-43
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: Q9ULW0
#3: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.57 Å3/Da / Density % sol: 52.23 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: CRYSTALS OF DEPHOSPHORYLATED A(122-403) IN COMPLEX WITH AMPPCP AND TPX2(1-43) WERE GROWN AT 18C BY VAPOR DIFFUSION AND THE HANGING DROP OBTAINED BY COMBINING 300UM DEP A(122-403) WITH 1.5MM ...Details: CRYSTALS OF DEPHOSPHORYLATED A(122-403) IN COMPLEX WITH AMPPCP AND TPX2(1-43) WERE GROWN AT 18C BY VAPOR DIFFUSION AND THE HANGING DROP OBTAINED BY COMBINING 300UM DEP A(122-403) WITH 1.5MM AMPPCP AND 300UM TPX2(1-43) WITH 0.2M LITHIUM SULFATE MONOHYDRATE, 0.1M BISTRIS PH5.5, 25% PEG3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.21433
DetectorType: ADSC QUANTUM 315 / 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: 1.21433 Å / Relative weight: 1
ReflectionResolution: 2.69→47.5 Å / Num. obs: 19139 / % possible obs: 100 % / Observed criterion σ(I): 2.3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.26 / Net I/σ(I): 8
Reflection shellResolution: 2.69→2.76 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.3 / % 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: 2.69→47.48 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.882 / SU B: 14.978 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28857 1035 5.4 %RANDOM
Rwork0.20066 ---
obs0.20526 18104 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.69→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4574 0 67 21 4662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194760
X-RAY DIFFRACTIONr_bond_other_d0.0020.024517
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9826448
X-RAY DIFFRACTIONr_angle_other_deg0.786310394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0325553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43922.807228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.87315826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1041540
X-RAY DIFFRACTIONr_chiral_restr0.0780.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215230
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021144
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: 2.694→2.764 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 88 -
Rwork0.284 1293 -
obs--100 %

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