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- PDB-6vph: TPX2 residues 7-20 fused to Aurora A residues 116-389 modified wi... -

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Basic information

Entry
Database: PDB / ID: 6vph
TitleTPX2 residues 7-20 fused to Aurora A residues 116-389 modified with cacodylate and in complex with AMP-PNP
ComponentsTPX2 fragment - Aurora A kinase domain fusion modified by cacodyate
KeywordsTRANSFERASE / Ser/Thr kinase
Function / homology
Function and homology information


Interaction between PHLDA1 and AURKA / microtubule nucleation / 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 / positive regulation of oocyte maturation / spindle pole centrosome ...Interaction between PHLDA1 and AURKA / microtubule nucleation / 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 / positive regulation of oocyte maturation / spindle pole centrosome / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / mitotic centrosome separation / meiotic spindle / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / spindle organization / intercellular bridge / positive regulation of mitochondrial fission / activation of protein kinase activity / mitotic spindle pole / regulation of G2/M transition of mitotic cell cycle / SUMOylation of DNA replication proteins / mitotic spindle assembly / spindle midzone / regulation of mitotic spindle organization / centriole / protein serine/threonine/tyrosine kinase activity / liver regeneration / AURKA Activation by TPX2 / positive regulation of mitotic nuclear division / positive regulation of mitotic cell cycle / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / ciliary basal body / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / negative regulation of protein binding / molecular function activator activity / 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 / mitotic spindle / kinetochore / G2/M transition of mitotic cell cycle / spindle pole / response to wounding / spindle / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / peptidyl-serine phosphorylation / basolateral plasma membrane / midbody / Regulation of TP53 Activity through Phosphorylation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein autophosphorylation / microtubule / molecular adaptor activity / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / protein phosphorylation / cell division / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ubiquitin protein ligase binding / glutamatergic synapse / negative regulation of apoptotic process / protein kinase binding / apoptotic process / 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. / Serine/Threonine protein kinases, catalytic domain / Protein kinase 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 / DITHIANE DIOL / Aurora kinase A / Targeting protein for Xklp2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.14 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,3729
Polymers34,2751
Non-polymers1,0988
Water3,153175
1
A: TPX2 fragment - Aurora A kinase domain fusion modified by cacodyate
hetero molecules

A: TPX2 fragment - Aurora A kinase domain fusion modified by cacodyate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,74518
Polymers68,5492
Non-polymers2,19516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area11260 Å2
ΔGint-94 kcal/mol
Surface area24230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.081, 89.081, 183.806
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein TPX2 fragment - Aurora A kinase domain fusion modified by cacodyate / 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: 34274.680 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

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Non-polymers , 5 types, 183 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-DTD / DITHIANE DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.07 Å3/Da / Density % sol: 59.95 % / Mosaicity: 0.7 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 6
Details: 0.1 M sodium cacodylate pH 6, 2 M NaCl, 9% PEG 3350

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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 RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 9, 2011 / 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: 2.14→30 Å / Num. obs: 24359 / % possible obs: 98.8 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.019 / Rrim(I) all: 0.065 / Χ2: 1.011 / Net I/σ(I): 49.5 / Num. measured all: 233292
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.14-2.223.50.28621390.8910.170.3351.02689.1
2.22-2.314.90.23423800.9490.1140.2611.0999.4
2.31-2.416.90.20624170.9760.0820.2231.057100
2.41-2.5410.50.17323990.9870.0540.1821.011100
2.54-2.710.90.14124420.9920.0440.1480.983100
2.7-2.910.70.11424160.9940.0360.121.042100
2.9-3.210.40.09224620.9960.0280.0970.99399.9
3.2-3.6610.60.07124640.9970.0220.0741.03399.8
3.661-4.6112.50.05525260.9980.0160.0571.03799.8
4.611-3013.50.0427140.9990.0110.0420.94399.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1ol5


Resolution: 2.14→29.54 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 1984 8.24 %
Rwork0.187 22097 -
obs0.1894 24081 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.2 Å2 / Biso mean: 44.5864 Å2 / Biso min: 22.87 Å2
Refinement stepCycle: final / Resolution: 2.14→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 65 175 2578
Biso mean--48.5 46.96 -
Num. residues----284
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 (%)
2.14-2.20.27181290.24171451158094
2.2-2.260.29031380.2311529166799
2.26-2.320.22841400.206915651705100
2.32-2.40.21851410.22621569171099
2.4-2.480.27781410.22811563170499
2.48-2.580.31151360.22091546168299
2.58-2.70.27131380.21261548168697
2.7-2.840.25851380.2261521165997
2.84-3.020.22151420.22231553169598
3.02-3.250.26541410.20191577171899
3.25-3.580.20411460.188116191765100
3.58-4.10.19971450.149116171762100
4.1-5.160.15581490.142516541803100
5.16-29.540.19421600.185517851945100
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)
11.5743-0.92331.05381.4159-0.42191.92450.01240.0331-0.1365-0.07770.07170.0364-0.07380.002100.240.0115-0.00940.2509-0.02390.267223.89924.01146.314
21.0048-0.24970.11190.878-0.85310.98680.0036-0.0293-0.267-0.28310.33820.24260.1042-0.06960.01540.3438-0.0052-0.02930.3280.07690.408626.27810.59957.992
31.0093-0.2866-0.5801-0.16570.32820.241-0.2038-0.06110.2843-0.01560.3039-0.27950.2879-0.12810.02510.4628-0.0206-0.01210.3554-0.02120.320641.3269.73740.889
41.6781-0.98731.63361.9365-0.42162.0291-0.0458-0.3668-0.3554-0.07230.20040.10360.2287-0.01880.09060.2828-0.0115-0.00480.17710.10730.310138.3432.51464.88
5-0.00220.0148-0.0089-0.0031-0.00480.03250.20050.980.1229-0.0407-0.1489-0.15810.78290.1452-0.00010.61040.0795-0.12640.6371-0.05140.396725.31919.98827.846
60.1-0.0315-0.07020.0519-0.06020.11260.12510.7127-0.4549-0.4152-0.5651-0.2035-0.095-0.1339-0.00190.4429-0.0128-0.09450.44070.0090.454518.19717.336.296
70.03730.06450.05680.13830.12270.1188-0.01660.3923-0.1498-0.4217-0.0981.0968-0.0125-0.3554-0.00720.2403-0.0122-0.00710.37920.00180.50118.00224.40946.151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 123:229 )A123 - 229
2X-RAY DIFFRACTION2( CHAIN A AND RESID 230:272 )A230 - 272
3X-RAY DIFFRACTION3( CHAIN A AND RESID 273:309 )A273 - 309
4X-RAY DIFFRACTION4( CHAIN A AND RESID 310:389 )A310 - 389
5X-RAY DIFFRACTION5( CHAIN A AND RESID -2:9 )A-2 - 9
6X-RAY DIFFRACTION6( CHAIN A AND RESID 10:14 )A10 - 14
7X-RAY DIFFRACTION7( CHAIN A AND RESID 15:116 )A15 - 116

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