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- PDB-5l8k: Aurora-A kinase domain in complex with vNAR-D01 (crystal form 2) -

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Basic information

Entry
Database: PDB / ID: 5l8k
TitleAurora-A kinase domain in complex with vNAR-D01 (crystal form 2)
Components
  • Aurora kinase A
  • New antigen receptor variable domain
KeywordsTRANSFERASE / kinase / vNAR / inhibitor
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 / chromosome passenger complex / positive regulation of oocyte maturation / mitotic centrosome separation / histone H3S10 kinase activity ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / chromosome passenger complex / positive regulation of oocyte maturation / mitotic centrosome separation / histone H3S10 kinase activity / pronucleus / germinal vesicle / meiotic spindle / protein localization to centrosome / anterior/posterior axis specification / neuron projection extension / spindle organization / centrosome localization / T cell receptor complex / positive regulation of mitochondrial fission / mitotic spindle pole / spindle midzone / SUMOylation of DNA replication proteins / negative regulation of protein binding / regulation of G2/M transition of mitotic cell cycle / centriole / liver regeneration / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic nuclear division / positive regulation of mitotic cell cycle / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / molecular function activator activity / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / AURKA Activation by TPX2 / 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 / peptidyl-serine phosphorylation / kinetochore / peptide antigen binding / response to wounding / spindle / G2/M transition of mitotic cell cycle / spindle pole / Regulation of PLK1 Activity at G2/M Transition / mitotic spindle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / microtubule cytoskeleton / protein autophosphorylation / midbody / Regulation of TP53 Activity through Phosphorylation / basolateral plasma membrane / adaptive immune response / proteasome-mediated ubiquitin-dependent protein catabolic process / microtubule / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / postsynaptic density / ciliary basal body / protein heterodimerization activity / negative regulation of gene expression / cell division / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / apoptotic process / centrosome / protein kinase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / glutamatergic synapse / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
: / Aurora kinase A / Aurora kinase / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...: / Aurora kinase A / Aurora kinase / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / 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 / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Aurora kinase A / New antigen receptor variable domain
Similarity search - Component
Biological speciesHomo sapiens (human)
Orectolobus maculatus (spotted wobbegong)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsBurgess, S.G. / Bayliss, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC24461/A13231 United Kingdom
CitationJournal: Open Biology / Year: 2016
Title: Allosteric inhibition of Aurora-A kinase by a synthetic vNAR domain.
Authors: Burgess, S.G. / Oleksy, A. / Cavazza, T. / Richards, M.W. / Vernos, I. / Matthews, D. / Bayliss, R.
History
DepositionJun 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aurora kinase A
B: New antigen receptor variable domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,97115
Polymers45,7312
Non-polymers1,24013
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-6 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.700, 109.720, 45.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-757-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#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: 32964.637 Da / Num. of mol.: 1 / Mutation: C290A, C393A
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: pET30TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Protein New antigen receptor variable domain


Mass: 12766.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orectolobus maculatus (spotted wobbegong)
Plasmid: pET26b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q8JJ25

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Non-polymers , 4 types, 293 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium sulfate, 0.1 M bis-Tris pH 5.5, 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 1.79→46.66 Å / Num. obs: 41932 / % possible obs: 97.8 % / Redundancy: 6.7 % / CC1/2: 1 / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.7
Reflection shellResolution: 1.79→1.84 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.2 / % possible all: 91.4

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CEG, 2COQ

4ceg

2coq


Resolution: 1.79→46.657 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.96
RfactorNum. reflection% reflection
Rfree0.2351 2042 4.87 %
Rwork0.1902 --
obs0.1924 41890 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.79→46.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2869 0 77 280 3226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073021
X-RAY DIFFRACTIONf_angle_d1.2274094
X-RAY DIFFRACTIONf_dihedral_angle_d13.8641083
X-RAY DIFFRACTIONf_chiral_restr0.05463
X-RAY DIFFRACTIONf_plane_restr0.004514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.83170.40091300.37862455X-RAY DIFFRACTION91
1.8317-1.87750.35611290.32822482X-RAY DIFFRACTION93
1.8775-1.92820.34241260.2852519X-RAY DIFFRACTION94
1.9282-1.9850.29591430.24652623X-RAY DIFFRACTION98
1.985-2.04910.27071330.21862646X-RAY DIFFRACTION99
2.0491-2.12230.25311370.20862689X-RAY DIFFRACTION99
2.1223-2.20730.23931360.20162679X-RAY DIFFRACTION99
2.2073-2.30770.25761380.19192605X-RAY DIFFRACTION97
2.3077-2.42940.23431480.19692693X-RAY DIFFRACTION100
2.4294-2.58160.21581250.2012699X-RAY DIFFRACTION100
2.5816-2.78090.27771530.19832705X-RAY DIFFRACTION100
2.7809-3.06070.22941500.19242728X-RAY DIFFRACTION100
3.0607-3.50340.20871260.17992672X-RAY DIFFRACTION97
3.5034-4.41340.19181360.14622772X-RAY DIFFRACTION100
4.4134-46.6730.23061320.18142881X-RAY DIFFRACTION98

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