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- PDB-8guw: Structure of Aurora Kinase A in complex with activator peptide -

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Basic information

Entry
Database: PDB / ID: 8guw
TitleStructure of Aurora Kinase A in complex with activator peptide
ComponentsPeptide from Centrosomal protein of 192 kDa,Aurora kinase A
KeywordsCYTOSOLIC PROTEIN / Complex / Kinase
Function / homology
Function and homology information


centrosome-templated microtubule nucleation / procentriole / procentriole replication complex / 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 ...centrosome-templated microtubule nucleation / procentriole / procentriole replication complex / 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 / pericentriolar material / mitotic spindle pole / centriole replication / SUMOylation of DNA replication proteins / mitotic spindle assembly / phosphatase binding / spindle midzone / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / 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 / response to bacterium / 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 / cytoplasm / cytosol
Similarity search - Function
Centrosomal protein Spd-2/CEP192 / 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. / Immunoglobulin-like fold ...Centrosomal protein Spd-2/CEP192 / 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. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Aurora kinase A / Centrosomal protein of 192 kDa
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLee, I.-G. / Park, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Sci Adv / Year: 2023
Title: Structural basis for CEP192-mediated regulation of centrosomal AURKA.
Authors: Park, J.G. / Jeon, H. / Shin, S. / Song, C. / Lee, H. / Kim, N.K. / Kim, E.E. / Hwang, K.Y. / Lee, B.J. / Lee, I.G.
History
DepositionSep 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Peptide from Centrosomal protein of 192 kDa,Aurora kinase A
B: Peptide from Centrosomal protein of 192 kDa,Aurora kinase A
C: Peptide from Centrosomal protein of 192 kDa,Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,6236
Polymers105,3423
Non-polymers1,2823
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11800 Å2
ΔGint-62 kcal/mol
Surface area41190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.859, 78.695, 185.634
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptide from Centrosomal protein of 192 kDa,Aurora kinase A / Cep192 / Cep192/SPD-2 / Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / ...Cep192 / Cep192/SPD-2 / Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-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: 35113.895 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Aurora Kinase A fused with activator peptide / Source: (gene. exp.) Homo sapiens (human)
Gene: CEP192, KIAA1569, PP8407, AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6
Production host: Escherichia coli (E. coli)
References: UniProt: Q8TEP8, UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 291 K / Method: liquid diffusion
Details: 0.1M Tris pH 8.0, 0.2M lithium sulfate, 15% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 26742 / % possible obs: 99.58 % / Redundancy: 9.4 % / CC1/2: 0.991 / CC star: 0.998 / Rpim(I) all: 0.03 / Net I/σ(I): 16.625
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 2635 / CC1/2: 0.693 / Rpim(I) all: 0.17

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DT3

5dt3


Resolution: 2.7→39.98 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 24.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2576 2000 7.48 %
Rwork0.2125 24732 -
obs0.2159 26732 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.39 Å2 / Biso mean: 59.3375 Å2 / Biso min: 18.57 Å2
Refinement stepCycle: final / Resolution: 2.7→39.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6743 0 81 74 6898
Biso mean--66.7 48.43 -
Num. residues----819
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.770.36761380.30731701183998
2.77-2.840.33831380.27781716185499
2.84-2.930.30371420.25831748189099
2.93-3.020.29661390.253417251864100
3.02-3.130.32251410.246117411882100
3.13-3.250.291420.241117591901100
3.25-3.40.28961430.232317641907100
3.4-3.580.28171410.225117451886100
3.58-3.810.2411420.218517601902100
3.81-4.10.25081440.190917731917100
4.1-4.510.2181430.178517671910100
4.51-5.160.21991450.173918001945100
5.16-6.50.27011470.22718201967100
6.5-39.980.21951550.187519132068100

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