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- PDB-5odt: Aurora-A in complex with TACC3 -

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Basic information

Entry
Database: PDB / ID: 5odt
TitleAurora-A in complex with TACC3
Components
  • Aurora kinase A
  • Transforming acidic coiled-coil-containing protein 3
KeywordsTRANSFERASE / Mitotic kinase
Function / homology
Function and homology information


microtubule cytoskeleton organization involved in mitosis / metaphase/anaphase transition of mitotic cell cycle / 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 ...microtubule cytoskeleton organization involved in mitosis / metaphase/anaphase transition of mitotic cell cycle / 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 / pronucleus / mitotic centrosome separation / germinal vesicle / meiotic spindle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / spindle organization / nuclear migration / positive regulation of mitochondrial fission / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / 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 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulation of NOTCH4 signaling / 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 / cerebral cortex development / kinetochore / response to wounding / centriolar satellite / microtubule cytoskeleton organization / 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 / 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 / intracellular membrane-bounded organelle / apoptotic process / centrosome / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm
Similarity search - Function
Transforming acidic coiled-coil-containing protein, C-terminal / TACC family / Transforming acidic coiled-coil-containing protein (TACC), C-terminal / 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 ...Transforming acidic coiled-coil-containing protein, C-terminal / TACC family / Transforming acidic coiled-coil-containing protein (TACC), C-terminal / 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
ADENOSINE-5'-DIPHOSPHATE / Aurora kinase A / Transforming acidic coiled-coil-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.021 Å
AuthorsBurgess, S.G. / Bayliss, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC24461/A12772 United Kingdom
CitationJournal: EMBO J. / Year: 2018
Title: Mitotic spindle association of TACC3 requires Aurora-A-dependent stabilization of a cryptic alpha-helix.
Authors: Burgess, S.G. / Mukherjee, M. / Sabir, S. / Joseph, N. / Gutierrez-Caballero, C. / Richards, M.W. / Huguenin-Dezot, N. / Chin, J.W. / Kennedy, E.J. / Pfuhl, M. / Royle, S.J. / Gergely, F. / Bayliss, R.
History
DepositionJul 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aurora kinase A
B: Transforming acidic coiled-coil-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,12510
Polymers38,0372
Non-polymers1,0888
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-65 kcal/mol
Surface area16670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.040, 137.040, 137.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

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Protein / Protein/peptide , 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: 32755.541 Da / Num. of mol.: 1 / Fragment: UNP residues 122-403 / Mutation: D274N, 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: pCDF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Protein/peptide Transforming acidic coiled-coil-containing protein 3 / ERIC-1


Mass: 5281.897 Da / Num. of mol.: 1 / Fragment: UNP residues 519-563
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TACC3, ERIC1 / Plasmid: pETM6T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q9Y6A5

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Non-polymers , 4 types, 148 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.82 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Bis-Tris pH 5.5, 2 M Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 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: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.021→68.52 Å / Num. obs: 28159 / % possible obs: 100 % / Redundancy: 20 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 25.9
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 20.5 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

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

4ceg


Resolution: 2.021→68.52 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.6
RfactorNum. reflection% reflection
Rfree0.2111 1330 4.72 %
Rwork0.1778 --
obs0.1794 28159 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.021→68.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 65 140 2571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082491
X-RAY DIFFRACTIONf_angle_d1.0473378
X-RAY DIFFRACTIONf_dihedral_angle_d14.512900
X-RAY DIFFRACTIONf_chiral_restr0.047364
X-RAY DIFFRACTIONf_plane_restr0.005423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0205-2.09280.31781340.26862655X-RAY DIFFRACTION100
2.0928-2.17660.27841380.22852660X-RAY DIFFRACTION100
2.1766-2.27560.27561280.20342639X-RAY DIFFRACTION100
2.2756-2.39560.23381180.20182693X-RAY DIFFRACTION100
2.3956-2.54570.22731170.22689X-RAY DIFFRACTION100
2.5457-2.74230.24851460.19722670X-RAY DIFFRACTION100
2.7423-3.01820.22141350.19182653X-RAY DIFFRACTION100
3.0182-3.4550.20861450.17552683X-RAY DIFFRACTION100
3.455-4.35280.18541210.15032703X-RAY DIFFRACTION100
4.3528-68.55940.18871480.16662784X-RAY DIFFRACTION100

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