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- PDB-6xka: TPX2 residues 7-20 fused to Aurora A residues 116-389 dephosphory... -

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Basic information

Entry
Database: PDB / ID: 6xka
TitleTPX2 residues 7-20 fused to Aurora A residues 116-389 dephosphorylated, and CoAlated on C290
ComponentsTPX2 fragment - Aurora A kinase domain fusion
KeywordsTRANSFERASE / Ser/Thr kinase
Function / homology
Function and homology information


microtubule nucleation / Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / negative regulation of microtubule depolymerization / axon hillock / importin-alpha family protein binding / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / positive regulation of oocyte maturation ...microtubule nucleation / Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / negative regulation of microtubule depolymerization / axon hillock / importin-alpha family protein binding / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / positive regulation of oocyte maturation / 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 / intercellular bridge / mitotic spindle pole / activation of protein kinase activity / SUMOylation of DNA replication proteins / mitotic spindle assembly / spindle midzone / regulation of mitotic spindle organization / regulation of G2/M transition of mitotic cell cycle / centriole / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic cell cycle / AURKA Activation by TPX2 / mitotic spindle organization / positive regulation of mitotic nuclear division / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / ciliary basal body / regulation of cytokinesis / negative regulation of protein binding / regulation of signal transduction by p53 class mediator / molecular function activator activity / liver regeneration / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / spindle microtubule / regulation of protein stability / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / spindle / kinetochore / mitotic spindle / response to wounding / spindle pole / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / basolateral plasma membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / peptidyl-serine phosphorylation / microtubule / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / postsynaptic density / molecular adaptor activity / 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 / cytosol
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 / Serine/threonine-protein kinase, active site ...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 / 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
Similarity search - Domain/homology
COENZYME A / Aurora kinase A / Targeting protein for Xklp2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsLim, D.C. / Yaffe, M.B.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES015339 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES028374 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES020466 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104047 United States
CitationJournal: Sci.Signal. / Year: 2020
Title: Redox priming promotes Aurora A activation during mitosis.
Authors: Lim, D.C. / Joukov, V. / Rettenmaier, T.J. / Kumagai, A. / Dunphy, W.G. / Wells, J.A. / Yaffe, M.B.
History
DepositionJun 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: TPX2 fragment - Aurora A kinase domain fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6742
Polymers33,9071
Non-polymers7681
Water46826
1
A: TPX2 fragment - Aurora A kinase domain fusion
hetero molecules

A: TPX2 fragment - Aurora A kinase domain fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3494
Polymers67,8142
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area5240 Å2
ΔGint-21 kcal/mol
Surface area25720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.310, 86.310, 76.834
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein TPX2 fragment - Aurora A kinase domain fusion / Targeting protein for Xklp2 / Aurora kinase A / Differentially expressed in cancerous and non- ...Targeting protein for Xklp2 / Aurora kinase A / Differentially expressed in cancerous and non-cancerous lung cells 2 / DIL-2 / Hepatocellular carcinoma-associated antigen 519 / Hepatocellular carcinoma-associated antigen 90 / Protein fls353 / Restricted expression proliferation-associated protein 100 / p100 / 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: 33906.754 Da / Num. of mol.: 1 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: TPX2, C20orf1, C20orf2, DIL2, HCA519, AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2
References: UniProt: Q9ULW0, UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.11 Å3/Da / Density % sol: 41.71 % / Mosaicity: 0.268 °
Crystal growTemperature: 298 K / Method: evaporation
Details: 0.2 M sodium citrate pH 4, 0.1 M sodium citrate pH 5.5, 18 mM sodium malonate pH 6, 4 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 27, 2019 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 8813 / % possible obs: 99.2 % / Redundancy: 6 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.028 / Rrim(I) all: 0.07 / Χ2: 1.718 / Net I/σ(I): 6.7 / Num. measured all: 53014
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.745.50.8078480.6320.3680.890.29599.2
2.74-2.856.40.5378600.8280.2260.5840.295100
2.85-2.986.30.3638640.9260.1540.3950.33499.9
2.98-3.1460.2438760.9580.1060.2650.36199.9
3.14-3.345.40.1368660.9840.0620.150.43499.4
3.34-3.66.60.0978820.9940.040.1050.54799.8
3.6-3.966.40.0648700.9950.0270.0690.72799.8
3.96-4.5360.0528900.9940.0230.0572.44299
4.53-5.715.80.0448930.9950.0190.0481.88598
5.71-505.70.0519640.9880.0220.0569.54597.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VPG

6vpg


Resolution: 2.65→47.79 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2789 879 10 %
Rwork0.2202 7910 -
obs0.2258 8789 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 197.79 Å2 / Biso mean: 96.7798 Å2 / Biso min: 43.98 Å2
Refinement stepCycle: final / Resolution: 2.65→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 881 0 2955
Biso mean--98.48 --
Num. residues----154
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.820.36111400.33571269140999
2.82-3.040.3321440.32413001444100
3.04-3.340.34451460.292913061452100
3.34-3.820.28311460.246313121458100
3.82-4.820.25091470.18851331147899
4.82-47.790.26481560.18941392154898
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.35540.44590.40210.48780.43650.5738-0.5818-1.290.02111.43520.2196-1.0064-0.67220.41120.00031.2844-0.00850.11060.9159-0.01520.72837.978535.40427.7705
22.248-2.1524-0.38422.7996-0.68851.5391-0.00830.4105-0.5065-0.24450.3976-0.79650.1402-0.08060.00061.0166-0.08910.0340.68620.00460.743312.597131.95719.1344
30.8003-0.8477-0.08280.87450.21580.17350.66980.1719-0.21370.4066-0.21060.4506-0.1587-1.35460.00030.7613-0.0522-0.04561.20760.06450.84193.448624.688718.693
41.9434-0.08890.1930.4644-0.12260.1052-0.1053-2.4003-0.93540.87930.43891.16432.429-0.866-0.01651.2797-0.18070.05891.04460.08931.23935.300714.732725.9896
50.1932-0.3403-0.00080.2993-0.13681.3993-0.2778-0.6090.3866-0.01930.6899-0.1083-0.12250.28660.00011.05440.00150.03410.81330.02410.715415.425921.29127.9274
60.03650.22180.23912.41050.52711.71270.69060.34710.741-0.6157-0.1503-0.0769-0.6202-0.7345-00.69440.0105-0.0050.78690.13480.732411.199426.86320.4598
71.4460.42651.57933.73271.65632.17570.2952-0.14920.0418-0.13530.2075-0.3920.12930.13360.00010.8753-0.10820.13240.61260.02250.804527.91513.024414.6758
81.1312-0.39470.4520.65710.11461.31730.162-0.51790.29770.2467-0.17620.1277-0.4187-0.4299-0.00020.8329-0.13380.05250.6380.02220.723719.404413.359819.2326
95.82981.5651-1.23760.7251-0.43270.420.36291.9290.96231.03320.08770.16230.5059-1.15010.05990.92-0.07630.1260.7727-0.01710.707515.072612.241123.0202
108.73872.7196-0.46165.9386-2.32022.90681.2007-0.74582.99281.5504-0.50120.76-0.78690.5431.10371.1564-0.06110.05130.9905-0.06881.1948-6.2292-14.714831.9962
110.16280.003-0.00290.07310.06370.04281.69110.15280.6226-0.8414-0.4265-1.8577-1.49970.60330.00581.0712-0.0438-0.2910.87030.1881.25251.4656-12.717626.4647
120.12410.77370.57477.93646.75335.92881.27140.4925-0.0502-1.7599-1.41991.41620.7861-1.2869-1.692.31770.6249-0.32361.16460.41690.820311.7242-4.377923.583
130.2598-0.2321-0.13861.11780.9530.69710.42410.23-0.0717-0.3406-0.34440.39510.0075-0.2814-0.00010.7785-0.03740.00160.61920.07360.772824.50434.856611.2132
140.19620.34680.39310.51150.14451.4587-0.45030.44130.0567-0.5361-0.33050.87170.0436-2.3076-0.00111.0335-0.0385-0.11661.1301-0.24940.873816.2970.3750.6054
152.3173-0.0050.86480.7970.8361.22940.14340.0058-0.68320.104-0.0974-0.25420.6543-0.08430.00010.7629-0.00170.0520.60310.01020.735327.8131-3.49819.8946
160.0985-0.13680.05220.3242-0.33510.22710.2806-0.1725-0.43881.0041-0.2813-0.4919-0.08920.55760.00020.84310.04410.00521.0268-0.07660.942134.97843.739520.2922
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 127 through 135 )A127 - 135
2X-RAY DIFFRACTION2chain 'A' and (resid 136 through 157 )A136 - 157
3X-RAY DIFFRACTION3chain 'A' and (resid 158 through 171 )A158 - 171
4X-RAY DIFFRACTION4chain 'A' and (resid 172 through 187 )A172 - 187
5X-RAY DIFFRACTION5chain 'A' and (resid 188 through 201 )A188 - 201
6X-RAY DIFFRACTION6chain 'A' and (resid 202 through 217 )A202 - 217
7X-RAY DIFFRACTION7chain 'A' and (resid 218 through 249 )A218 - 249
8X-RAY DIFFRACTION8chain 'A' and (resid 250 through 269 )A250 - 269
9X-RAY DIFFRACTION9chain 'A' and (resid 270 through 280 )A270 - 280
10X-RAY DIFFRACTION10chain 'A' and (resid 291 through 295 )A291 - 295
11X-RAY DIFFRACTION11chain 'A' and (resid 296 through 301 )A296 - 301
12X-RAY DIFFRACTION12chain 'A' and (resid 302 through 309 )A302 - 309
13X-RAY DIFFRACTION13chain 'A' and (resid 310 through 324 )A310 - 324
14X-RAY DIFFRACTION14chain 'A' and (resid 325 through 342 )A325 - 342
15X-RAY DIFFRACTION15chain 'A' and (resid 343 through 373 )A343 - 373
16X-RAY DIFFRACTION16chain 'A' and (resid 374 through 388 )A374 - 388

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