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- PDB-6vpi: TPX2 residues 7-20 fused to Aurora A residues 116-389 C247V + D25... -

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Basic information

Entry
Database: PDB / ID: 6vpi
TitleTPX2 residues 7-20 fused to Aurora A residues 116-389 C247V + D256N + C319V triple mutant disulfide homodimer in complex with AMP-PNP
ComponentsTPX2 fragment - Aurora A kinase domain fusion
KeywordsTRANSFERASE / Ser/Thr kinase
Function / homology
Function and homology information


nuclear microtubule / microtubule nucleation / Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / importin-alpha family protein binding / negative regulation of microtubule depolymerization / spindle assembly involved in female meiosis I / cilium disassembly / positive regulation of oocyte maturation ...nuclear microtubule / microtubule nucleation / Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / importin-alpha family protein binding / negative regulation of microtubule depolymerization / 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 / intercellular bridge / activation of protein kinase activity / protein kinase activator activity / mitotic spindle pole / 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 / 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 / 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 / spindle pole / 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 / microtubule binding / basolateral plasma membrane / peptidyl-serine phosphorylation / proteasome-mediated ubiquitin-dependent protein catabolic process / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / molecular adaptor activity / 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 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / MALONIC ACID / Aurora kinase A / Targeting protein for Xklp2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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
DepositionFeb 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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)34,5575
Polymers33,8981
Non-polymers6594
Water4,197233
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)69,11310
Polymers67,7952
Non-polymers1,3188
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area7270 Å2
ΔGint-78 kcal/mol
Surface area24650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.292, 85.292, 128.246
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-907-

HOH

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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: 33897.742 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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 3.44 Å3/Da / Density % sol: 64.25 % / Mosaicity: 0.359 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 7
Details: 0.336 M sodium malonate pH 7.5, 0.348 M sodium malonate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 16, 2015 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→23.33 Å / Num. obs: 32094 / % possible obs: 98.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.026 / Rrim(I) all: 0.054 / Χ2: 0.988 / Net I/σ(I): 13.9 / Num. measured all: 126757
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.70.61715620.790.3550.7140.90497.5
2.03-2.073.90.53615800.8230.3030.6180.88598.4
2.07-2.113.90.45115700.8690.2530.5190.94498.7
2.11-2.153.90.39315710.9050.2210.4520.98698.8
2.15-2.23.90.36416060.9270.2030.4180.94898.8
2.2-2.2540.28515890.9460.160.3281.0198.7
2.25-2.3140.25415880.9580.1430.2930.98399.3
2.31-2.3740.20816230.9680.1160.2390.98599.1
2.37-2.4440.19215770.9760.1080.221.03999
2.44-2.5240.15715980.9840.0880.181.02398.9
2.52-2.6140.13516010.9880.0760.1551.08499.1
2.61-2.7140.11115930.9910.0620.1271.09998.7
2.71-2.8440.08716200.9930.0480.11.03898.7
2.84-2.9940.06716050.9960.0380.0770.9998.4
2.99-3.1740.05416180.9980.030.0621.02998.3
3.17-3.4240.03916080.9980.0220.0450.96397.9
3.42-3.7640.0316260.9990.0160.0341.0298
3.76-4.340.02216330.9990.0120.0250.98497.8
4.3-5.413.90.019165810.010.0210.91897.5
5.41-23.333.90.01816680.9990.0090.0210.91191.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OL5

1ol5


Resolution: 2→23.26 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.25
RfactorNum. reflection% reflection
Rfree0.215 1995 6.23 %
Rwork0.186 --
obs0.1878 32025 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.3 Å2 / Biso mean: 41.7298 Å2 / Biso min: 20.54 Å2
Refinement stepCycle: final / Resolution: 2→23.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 40 233 2558
Biso mean--72.43 49.54 -
Num. residues----278
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 (%)
2-2.050.29861390.26222094223398
2.05-2.110.29971400.23442102224299
2.11-2.170.26981420.23392126226899
2.17-2.240.26511410.22522130227199
2.24-2.320.22981420.22262137227999
2.32-2.410.28241430.22322138228199
2.41-2.520.23771420.22222138228099
2.52-2.650.22841430.22912139228299
2.65-2.820.261390.22192143228299
2.82-3.040.23431430.21722160230398
3.04-3.340.25921440.19372156230098
3.34-3.820.20381440.15782160230498
3.82-4.810.14931460.13172192233898
4.81-23.260.18131470.17062215236293
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)
10.2525-0.52810.16091.7288-0.10930.5624-0.0693-0.0455-0.05160.2590.06860.09510.0744-0.0170.00180.3288-0.01020.03730.1969-0.02560.2474-28.263-4.4126.94
20.0250.01530.01590.01110.0170.0469-0.14430.2448-0.1379-0.30040.1644-0.0664-0.20430.16090.00010.3394-0.0082-0.010.4247-0.07350.3801-17.69819.13937.645
30.33080.4340.07031.7770.22871.1453-0.00380.04260.0671-0.0729-0.00860.0199-0.161-0.0513-00.3010.0074-0.0260.2074-0.02380.2564-26.3214.46412.217
40.0756-0.12270.05130.1999-0.07420.1227-0.1884-0.2831-0.19320.62390.16790.4621-0.1036-0.28660.00130.7361-0.01760.21640.43810.0020.5268-35.413-11.00538.616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 126:287 )A126 - 287
2X-RAY DIFFRACTION2( CHAIN A AND RESID 288:307 )A288 - 307
3X-RAY DIFFRACTION3( CHAIN A AND RESID 308:389 )A308 - 389
4X-RAY DIFFRACTION4( CHAIN A AND RESID 7:20 )A7 - 20

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