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- PDB-6vpg: TPX2 residues 7-20 fused to Aurora A residues 116-389 in complex ... -

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Basic information

Entry
Database: PDB / ID: 6vpg
TitleTPX2 residues 7-20 fused to Aurora A residues 116-389 in complex with AMP-PNP
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 / positive regulation of mitochondrial fission / spindle organization / 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 / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of mitotic nuclear division / ciliary basal body / negative regulation of protein binding / regulation of cytokinesis / 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 / 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 / spindle / kinetochore / spindle pole / response to wounding / 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / basolateral plasma membrane / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / microtubule / postsynaptic density / protein autophosphorylation / molecular adaptor activity / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / cell division / negative regulation of gene expression / protein phosphorylation / 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 / Aurora kinase A / Targeting protein for Xklp2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.64 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)34,7606
Polymers34,0671
Non-polymers6945
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.562, 83.562, 114.516
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#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: 34066.715 Da / Num. of mol.: 1 / Fragment: kinase domain,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, 68 molecules

#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.93 Å3/Da / Density % sol: 58.08 % / Mosaicity: 0.705 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 7
Details: 0.1 M HEPES pH 7, 0.9 M KCl, 1.08 M ammonium sulfate, 12% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 12, 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: 2.64→30 Å / Num. obs: 12410 / % possible obs: 99.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.037 / Rrim(I) all: 0.083 / Χ2: 1.057 / Net I/σ(I): 25.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.744.80.90412110.7460.4561.0151.07999.6
2.74-2.8550.62212050.8240.3050.6941.076100
2.85-2.9850.42412120.920.2060.4721.07999.9
2.98-3.145.10.27112140.9570.1310.3021.06100
3.14-3.345.10.17512270.9840.0850.1951.06899.9
3.34-3.650.12112250.9890.0590.1351.01599.9
3.6-3.9650.0912410.9920.0440.1011.051100
3.96-4.5350.05912360.9950.0290.0661.00299.8
4.53-5.74.90.0512860.9960.0250.0561.087100
5.7-304.60.03213530.9990.0170.0361.05298.5

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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: 2.64→27.08 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.68
RfactorNum. reflection% reflection
Rfree0.2453 1238 10.01 %
Rwork0.1991 --
obs0.2037 12369 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 215.38 Å2 / Biso min: 42.59 Å2
Refinement stepCycle: final / Resolution: 2.64→27.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2323 0 169 63 2555
Biso mean--108.94 71.3 -
Num. residues----266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.64-2.750.35381330.31611192132599
2.75-2.880.37131360.294812251361100
2.88-3.030.33721330.273712021335100
3.03-3.220.32861360.258212261362100
3.22-3.460.28691360.233212161352100
3.46-3.810.25321370.206112341371100
3.81-4.360.2021370.163412311368100
4.36-5.490.16821410.15912681409100
5.49-27.080.25171490.18571337148699
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)
10.0157-0.0395-0.02010.09310.07050.1092-0.07190.05430.0804-0.31840.0075-0.00640.1020.04270.00480.6077-0.26880.2641.4663-0.02881.28598.01627.1847.644
20.02320.01430.0165-0.0126-0.00330.03680.070.31620.1237-0.4650.3676-0.4045-0.08910.518300.62280.02330.04480.9682-0.09511.13554.97914.57421.613
30.09210.0267-0.10430.03580.06360.9421-0.33561.3273-0.4058-0.56450.3018-0.40870.79420.05630.1310.5814-0.10990.19280.7971-0.0760.5828-3.30815.6639.556
41.1334-1.7141-0.47072.2591-0.57692.7401-0.0926-0.0413-0.03180.24370.3473-0.0559-0.4950.07340.21820.5555-0.15280.0810.3520.03390.4953-13.83837.31117.282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 7:11 )A7 - 11
2X-RAY DIFFRACTION2( CHAIN A AND RESID 12:117 )A12 - 117
3X-RAY DIFFRACTION3( CHAIN A AND RESID 124:171 )A124 - 171
4X-RAY DIFFRACTION4( CHAIN A AND RESID 172:389 )A172 - 389

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