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- PDB-5lxm: Crystal structure of Aurora-A bound to a hydrocarbon-stapled prot... -

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Basic information

Entry
Database: PDB / ID: 5lxm
TitleCrystal structure of Aurora-A bound to a hydrocarbon-stapled proteomimetic of TPX2
Components
  • Aurora kinase A
  • Targeting protein for Xklp2
KeywordsTRANSFERASE / Protein kinase / Proteomimetic / Stapled helix peptide / Mitosis
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 / Transferase(Phosphotransferase) domain 1 ...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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / AMMONIA / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / DI(HYDROXYETHYL)ETHER / Aurora kinase A / Targeting protein for Xklp2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsMcIntyre, P.J. / Bayliss, R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K016903/1 United Kingdom
Cancer Research UKC24461/A12772 United Kingdom
CitationJournal: ACS Chem. Biol. / Year: 2016
Title: A TPX2 Proteomimetic Has Enhanced Affinity for Aurora-A Due to Hydrocarbon Stapling of a Helix.
Authors: Rennie, Y.K. / McIntyre, P.J. / Akindele, T. / Bayliss, R. / Jamieson, A.G.
History
DepositionSep 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aurora kinase A
D: Targeting protein for Xklp2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,58913
Polymers37,2012
Non-polymers1,38811
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-39 kcal/mol
Surface area13510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.780, 79.780, 140.260
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AD

#1: Protein Aurora kinase A / / Aurora 2 / Aurora/IPL1-related kinase 1 / hARK1 / Breast tumor-amplified kinase / Serine/threonine- ...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: 32836.508 Da / Num. of mol.: 1 / Mutation: C290A, C393A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6
Production host: Escherichia coli (E. coli)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Protein/peptide Targeting protein for Xklp2 / Differentially expressed in cancerous and non-cancerous lung cells 2 / DIL-2 / Hepatocellular ...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


Mass: 4364.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9ULW0

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Non-polymers , 10 types, 88 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Diethylene glycol diethyl ether


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#9: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#11: Chemical ChemComp-NH3 / AMMONIA / Differentially expressed in cancerous and non-cancerous lung cells 2 / DIL-2 / Hepatocellular ...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 / Ammonia


Mass: 17.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH3 / Source: (synth.) Homo sapiens (human)
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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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: 66.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: MORPHEUS Crystallization Screen condition C1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.08→61.98 Å / Num. obs: 31554 / % possible obs: 99.4 % / Redundancy: 9.6 % / Net I/σ(I): 9.94

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.2data extraction
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CEG

4ceg


Resolution: 2.08→61.98 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.13
RfactorNum. reflection% reflection
Rfree0.2429 1602 5.08 %
Rwork0.1996 --
obs0.2018 31526 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 169.8 Å2 / Biso mean: 74.378 Å2 / Biso min: 37.48 Å2
Refinement stepCycle: final / Resolution: 2.08→61.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 85 77 2582
Biso mean--96.19 66.44 -
Num. residues----301
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)
12.50611.65270.9431.43980.16789.26840.66061.43770.1701-1.033-0.42750.0909-1.58240.2503-0.19141.24020.45790.05471.01770.03680.460644.3288-0.46054.9321
27.414-2.23992.40454.606-0.10567.2480.14880.78240.3781-0.3136-0.19340.0927-1.6278-0.74130.15190.9790.20530.13080.65150.04240.366245.4526-1.92746.1031
34.0051-1.0571-3.69424.8779-0.58615.67510.43280.8040.0535-0.792-0.5265-0.2232-0.8537-0.48890.09190.6390.18940.05270.8040.00830.346647.7404-14.5042.2049
43.0054-1.9471-2.7794.129-2.15418.05590.07690.00120.1690.6573-0.08720.1588-0.85310.16780.00290.71230.11130.04850.647-0.05770.380844.269-9.772917.1404
56.97280.1431.33724.6476-3.22128.8121-0.03850.8399-0.89830.3546-0.11450.51680.0636-1.42660.12260.36250.01890.07280.4838-0.14510.514641.1669-26.615916.4901
67.3088-6.5604-6.32735.92136.57268.2372-0.23560.0219-0.0580.49810.1933-0.03840.03040.0752-0.0530.55410.05650.06110.5171-0.04250.355946.3099-19.135714.3136
75.788-3.2392-2.43573.465-0.26855.07740.35871.1181-0.1583-0.0895-0.468-0.0572-0.32470.31080.14010.39440.0421-0.0440.8374-0.12250.30754.8994-23.30016.6908
87.0177-1.5462-1.36363.789-1.61632.8578-0.42410.0854-0.37720.4294-0.04890.0865-0.20260.07120.42530.51480.03880.03850.5528-0.03340.358556.3319-26.87718.7879
99.6347-4.3188-3.13398.22050.55063.3593-0.4598-0.37341.02831.39120.2501-1.0344-0.1340.80450.22560.83440.0766-0.1420.6983-0.00970.444563.8247-22.757527.3874
108.0292.8623-3.66244.1471-3.11426.3059-0.5826-1.202-0.47221.02630.25230.20630.10750.1610.29150.96240.27510.17350.62160.07480.49451.1755-32.496131.0889
113.2405-2.235-3.81454.1690.36299.1654-0.37650.9076-1.52390.72120.00930.88960.8306-0.9730.46010.6314-0.07370.2150.4023-0.13160.623944.8878-34.875719.733
122.8199-1.4471-2.13076.2261-4.09826.59690.87172.7928-0.4633-3.23330.3918-2.2087-2.81330.1009-1.47911.0472-0.01780.34651.1517-0.00540.666655.0643-8.9193-5.8914
132.2457-1.32242.37546.681-0.75333.23090.05210.6747-0.0416-0.4256-0.68061.38140.5661-0.68150.50410.94830.2431-0.02751.7635-0.21360.626836.1666-11.3314-3.6083
146.5902-6.5617-6.81378.95966.01796.88460.4102-0.6725-0.7575-0.2491-1.0850.5542-0.2808-1.61720.65340.49460.141-0.02941.2702-0.21370.464548.0302-26.0654-6.7796
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 126 through 145 )A126 - 145
2X-RAY DIFFRACTION2chain 'A' and (resid 146 through 171 )A146 - 171
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 201 )A172 - 201
4X-RAY DIFFRACTION4chain 'A' and (resid 202 through 229 )A202 - 229
5X-RAY DIFFRACTION5chain 'A' and (resid 230 through 250 )A230 - 250
6X-RAY DIFFRACTION6chain 'A' and (resid 251 through 269 )A251 - 269
7X-RAY DIFFRACTION7chain 'A' and (resid 270 through 292 )A270 - 292
8X-RAY DIFFRACTION8chain 'A' and (resid 293 through 324 )A293 - 324
9X-RAY DIFFRACTION9chain 'A' and (resid 325 through 343 )A325 - 343
10X-RAY DIFFRACTION10chain 'A' and (resid 344 through 363 )A344 - 363
11X-RAY DIFFRACTION11chain 'A' and (resid 364 through 392 )A364 - 392
12X-RAY DIFFRACTION12chain 'D' and (resid 6 through 10 )D6 - 10
13X-RAY DIFFRACTION13chain 'D' and (resid 11 through 30 )D11 - 30
14X-RAY DIFFRACTION14chain 'D' and (resid 31 through 43 )D31 - 43

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