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- PDB-6vpj: TPX2 residues 7-20 fused to Aurora A residues 116-389 C247V + C31... -

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Basic information

Entry
Database: PDB / ID: 6vpj
TitleTPX2 residues 7-20 fused to Aurora A residues 116-389 C247V + C319V double mutant dephosphorylated, and 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
trehalose / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Aurora kinase A / Targeting protein for Xklp2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)34,7473
Polymers33,8991
Non-polymers8482
Water2,036113
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)69,4946
Polymers67,7972
Non-polymers1,6974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7590 Å2
ΔGint-34 kcal/mol
Surface area29380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.941, 90.941, 118.882
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: 33898.730 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: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 3.63 Å3/Da / Density % sol: 66.07 % / Mosaicity: 0.329 °
Crystal growTemperature: 298 K / Method: evaporation
Details: 0.2 M sodium citrate pH 4, 0.8 M sodium citrate pH 5.5, 6% PEG 3350, 8% trehalose

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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: 2.1→50 Å / Num. obs: 29631 / % possible obs: 100 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.015 / Rrim(I) all: 0.054 / Χ2: 0.898 / Net I/σ(I): 8.2 / Num. measured all: 363214
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1812.21.8429010.5210.5451.9210.404100
2.18-2.2612.91.02629050.7920.2961.0680.439100
2.26-2.3712.40.70628930.9110.2080.7360.407100
2.37-2.4911.20.41529120.9550.1290.4350.436100
2.49-2.6512.20.24629360.9820.0730.2570.485100
2.65-2.8513.30.14529420.9950.0410.1510.581100
2.85-3.1412.70.0929620.9980.0260.0940.864100
3.14-3.5911.50.06229600.9990.0190.0651.58100
3.59-4.5212.50.04330310.9990.0130.0452.108100
4.52-5011.70.0331890.9990.0090.0311.62499.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1000246823

Resolution: 2.1→45.47 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2146 2000 6.76 %
Rwork0.1898 27572 -
obs0.1915 29572 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.83 Å2 / Biso mean: 72.2211 Å2 / Biso min: 44.09 Å2
Refinement stepCycle: final / Resolution: 2.1→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2289 0 1105 113 3507
Biso mean--72.83 72.15 -
Num. residues----160
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.160.30661390.317119302069
2.16-2.220.29481410.286219282069
2.22-2.280.30671390.274119262065
2.28-2.350.2661400.254119312071
2.35-2.440.30551410.243819422083
2.44-2.540.26171430.236619612104
2.54-2.650.25321400.236219312071
2.65-2.790.27881410.228719532094
2.79-2.970.29811420.231419592101
2.97-3.190.26051440.222919692113
3.2-3.520.23711440.212419872131
3.52-4.020.18421440.16919822126
4.03-5.070.15871470.141420322179
5.07-45.470.19761550.174521412296
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)
10.92150.1240.2506-0.1125-0.01060.06040.12260.2562-1.1544-0.7001-0.0913-0.27480.4527-0.31120.0111.17850.02080.14740.6278-0.11470.82229.3923-18.4056-8.353
20.7380.6574-0.27720.8454-0.21311.5114-0.05630.1362-0.0949-0.05660.08440.59420.2582-0.416400.94610.0049-0.00060.54310.0210.742321.517-13.85521.687
30.62240.67370.16191.25230.54610.31710.1550.3451-0.5005-0.44060.12830.32250.21980.0472-0.00010.8602-0.0269-0.12030.59710.06890.719918.8868-8.2473-5.8687
40.728-0.1201-0.46770.6973-0.40320.49530.16480.67740.3507-1.21910.18110.03190.61960.2037-0.00011.05050.0237-0.05460.75280.13330.735125.63051.7742-10.3025
51.15710.2147-0.64850.918-0.51860.4261-0.18890.2269-0.193-0.87130.1991-0.3141-0.00380.30110.00010.87920.03910.00090.55130.04020.680932.6416-4.9664-1.9947
60.28430.40270.02341.1238-0.93230.91170.05660.1078-0.11-0.02730.04480.2370.51250.172300.90770.0215-0.0910.5630.01720.690323.375-9.7224-0.7138
70.3735-0.0376-0.59680.6237-0.05980.90010.0757-0.075-0.27880.22170.14120.27820.3471-0.66670.00030.79850.00730.030.62570.10810.689921.35782.59120.4757
81.4239-0.5180.1250.8060.63850.6528-0.0536-0.1342-0.00410.2443-0.1287-0.3491-0.31720.7127-0.00020.70270.0016-0.04740.60660.09630.648535.30697.212.1189
90.3737-0.66080.26360.8718-0.26050.84970.12020.75610.65450.1812-0.01870.0176-0.1333-0.8411-0.00010.682-0.03180.00350.78690.07780.653129.609910.2960.4709
100.77690.7957-0.17580.7534-0.02590.1903-0.08360.1356-0.61490.01730.17360.28280.30830.09430.00010.79320.0588-0.04690.53070.05220.658228.4483-0.426311.1829
110.1067-0.00670.1878-0.02180.00090.11740.12450.2736-0.0828-0.89740.0783-0.78230.1026-0.01260.00041.04450.08070.02890.73290.06130.756418.90375.5522-3.3009
120.0863-0.04720.10460.46580.20460.15870.1193-0.7397-0.3473-0.0596-0.5167-0.2732-0.1933-1.0386-0.04090.5112-0.08850.00110.93370.11970.658614.570117.0091-7.6453
131.5586-1.18881.00060.8068-1.01830.6545-0.06020.22680.2082-0.004-0.1784-0.33420.16720.36520.00010.6453-0.0485-0.0950.52610.07820.622429.367817.54295.913
140.1623-0.3329-0.22990.48430.43810.2858-0.3737-0.41910.6047-0.0870.42890.15250.3031-1.30830.00010.8513-0.0128-0.13880.78440.06230.656815.593218.405917.1005
150.09020.0184-0.06050.4112-0.33850.24550.7913-0.05910.36231.0296-0.26910.2517-0.1091-0.0322-0.00030.7320.0659-0.14950.5061-0.02320.706715.007125.651210.8072
161.5727-1.04450.65712.22890.85941.5558-0.0833-0.40720.75730.4550.0065-0.5105-0.54560.3180.00010.7602-0.0461-0.19270.4999-0.01150.67230.313722.267719.0707
170.49570.0978-0.00370.20450.24380.3157-0.3752-0.64250.11110.39580.0412-1.0927-0.36410.8647-0.00020.6590.0207-0.15850.77310.10110.815840.772711.503818.5869
180.00570.0072-0.01580.02790.07910.1663-1.10980.93190.7414-1.20511.2512-2.0728-0.07581.06910.00091.0436-0.03410.10391.44280.21280.808141.404822.3706-47.2414
190.11950.0155-0.04970.05650.08510.09760.03281.1162-1.58670.59680.53530.64110.89290.0525-0.00011.03260.0531-0.01931.2099-0.08810.911137.916512.2175-41.8265
200.0524-0.043-0.07550.03840.04520.10410.18680.8943-1.5178-0.3470.06160.04410.83120.7404-00.7945-0.04960.09890.9666-0.16271.045328.13188.3675-33.0672
211.99992.000122.00032.00031.99990.5309-3.8751-4.05083.88981.62527.2657-0.8387-14.3648-1.82691.5062-0.13390.13832.3907-0.30681.148928.78492.2032-29.116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 124 through 135 )A124 - 135
2X-RAY DIFFRACTION2chain 'A' and (resid 136 through 156 )A136 - 156
3X-RAY DIFFRACTION3chain 'A' and (resid 157 through 172 )A157 - 172
4X-RAY DIFFRACTION4chain 'A' and (resid 173 through 187 )A173 - 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 229 )A218 - 229
8X-RAY DIFFRACTION8chain 'A' and (resid 230 through 249 )A230 - 249
9X-RAY DIFFRACTION9chain 'A' and (resid 250 through 258 )A250 - 258
10X-RAY DIFFRACTION10chain 'A' and (resid 259 through 272 )A259 - 272
11X-RAY DIFFRACTION11chain 'A' and (resid 273 through 283 )A273 - 283
12X-RAY DIFFRACTION12chain 'A' and (resid 287 through 297 )A287 - 297
13X-RAY DIFFRACTION13chain 'A' and (resid 298 through 324 )A298 - 324
14X-RAY DIFFRACTION14chain 'A' and (resid 325 through 333 )A325 - 333
15X-RAY DIFFRACTION15chain 'A' and (resid 334 through 342 )A334 - 342
16X-RAY DIFFRACTION16chain 'A' and (resid 343 through 373 )A343 - 373
17X-RAY DIFFRACTION17chain 'A' and (resid 374 through 389 )A374 - 389
18X-RAY DIFFRACTION18chain 'A' and (resid -1 through 10 )A-1 - 10
19X-RAY DIFFRACTION19chain 'A' and (resid 11 through 15 )A11 - 15
20X-RAY DIFFRACTION20chain 'A' and (resid 16 through 20 )A16 - 20
21X-RAY DIFFRACTION21chain 'A' and (resid 116 through 116 )A116

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