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- PDB-5ap0: Naturally Occurring Mutations in the MPS1 Gene Predispose Cells t... -

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Basic information

Entry
Database: PDB / ID: 5ap0
TitleNaturally Occurring Mutations in the MPS1 Gene Predispose Cells to Kinase Inhibitor Drug Resistance.
ComponentsDUAL SPECIFICITY PROTEIN KINASE TTK
KeywordsTRANSFERASE / MPS1 / PROTEIN KINASE / MITOSIS / DRUG RESISTANCE
Function / homology
Function and homology information


protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / repair of mitotic kinetochore microtubule attachment defect / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / positive regulation of SMAD protein signal transduction ...protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / repair of mitotic kinetochore microtubule attachment defect / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / positive regulation of SMAD protein signal transduction / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization / chromosome segregation / kinetochore / spindle / protein tyrosine kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / ATP binding / identical protein binding / nucleus / membrane / cytoplasm
Similarity search - Function
Protein kinase Mps1 family / Tetratricopeptide-like helical domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 Mps1 family / Tetratricopeptide-like helical domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
Chem-AU5 / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGurden, M.D. / Westwood, I.M. / Faisal, A. / Naud, S. / Cheung, K.J. / McAndrew, C. / Wood, A. / Schmitt, J. / Boxall, K. / Mak, G. ...Gurden, M.D. / Westwood, I.M. / Faisal, A. / Naud, S. / Cheung, K.J. / McAndrew, C. / Wood, A. / Schmitt, J. / Boxall, K. / Mak, G. / Workman, P. / Burke, R. / Hoelder, S. / Blagg, J. / van Montfort, R.L.M. / Linardopoulos, S.
CitationJournal: Cancer Res. / Year: 2015
Title: Naturally Occurring Mutations in the Mps1 Gene Predispose Cells to Kinase Inhibitor Drug Resistance.
Authors: Gurden, M.D. / Westwood, I.M. / Faisal, A. / Naud, S. / Cheung, K.J. / Mcandrew, C. / Wood, A. / Schmitt, J. / Boxall, K. / Mak, G. / Workman, P. / Burke, R. / Hoelder, S. / Blagg, J. / Van ...Authors: Gurden, M.D. / Westwood, I.M. / Faisal, A. / Naud, S. / Cheung, K.J. / Mcandrew, C. / Wood, A. / Schmitt, J. / Boxall, K. / Mak, G. / Workman, P. / Burke, R. / Hoelder, S. / Blagg, J. / Van Montfort, R.L.M. / Linardopoulos, S.
History
DepositionSep 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUAL SPECIFICITY PROTEIN KINASE TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,33820
Polymers36,1951
Non-polymers2,14319
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.930, 111.960, 113.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2005-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DUAL SPECIFICITY PROTEIN KINASE TTK / PHOSPHOTYROSINE PICKED THREONINE-PROTEIN KINASE / PYT / MONOPOLAR SPINDLE KINASE 1


Mass: 36195.234 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, UNP RESIDUES 519-808
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI / References: UniProt: P33981, dual-specificity kinase

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Non-polymers , 5 types, 78 molecules

#2: Chemical ChemComp-AU5 / 9-CYCLOPENTYL-2-[[2-METHOXY-4-[(1-METHYLPIPERIDIN-4-YL)OXY]-PHENYL]AMINO]-7-METHYL-7,9-DIHYDRO-8H-PURIN-8-ONE


Mass: 452.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32N6O3
#3: Chemical ChemComp-P4C / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / POLYETHYLENE 400


Mass: 324.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O8
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer details2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL (7 9-CYCLOPENTYL-2-[[2-METHOXY-4- ...2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL (7 9-CYCLOPENTYL-2-[[2-METHOXY-4-[(1-METHYLPIPERIDIN-4-YL)OXY]-PHENYL]A
Sequence detailsTHE SEQUENCE INCLUDING HEXAHISTIDINE TAG IS AS DESCRIBED IN NAT. CHEM. BIOL. 2010, 6, 259-368.

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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: 3.1 Å3/Da / Density % sol: 60.34 % / Description: NONE
Crystal growpH: 7.5 / Details: 30% (V/V) PEG300, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793
DetectorType: QUANTUM / Detector: CCD / Date: Aug 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.15→41.12 Å / Num. obs: 23736 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 58.67 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.9
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 0.7 / % possible all: 72.9

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C4J

4c4j


Resolution: 2.15→41.12 Å / Cor.coef. Fo:Fc: 0.9567 / Cor.coef. Fo:Fc free: 0.9514 / SU R Cruickshank DPI: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.155 / SU Rfree Blow DPI: 0.145 / SU Rfree Cruickshank DPI: 0.147
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 1206 5.09 %RANDOM
Rwork0.1842 ---
obs0.1861 23673 95.17 %-
Displacement parametersBiso mean: 74.03 Å2
Baniso -1Baniso -2Baniso -3
1-2.2875 Å20 Å20 Å2
2---1.9008 Å20 Å2
3----0.3867 Å2
Refine analyzeLuzzati coordinate error obs: 0.306 Å
Refinement stepCycle: LAST / Resolution: 2.15→41.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2025 0 135 59 2219
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012191HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.092934HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d768SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes56HARMONIC2
X-RAY DIFFRACTIONt_gen_planes317HARMONIC5
X-RAY DIFFRACTIONt_it2191HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion19.4
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion279SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2551SEMIHARMONIC4
LS refinement shellResolution: 2.15→2.25 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2286 105 4.87 %
Rwork0.2428 2050 -
all0.2421 2155 -
obs--95.17 %
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)
17.504-2.4152-0.19426.5155-1.62683.55290.0619-0.5442-0.54420.12260.1970.32190.5442-0.4598-0.2589-0.263-0.0231-0.0417-0.24020.1520.3028-10.10268.8858-20.8115
26.48961.32321.39553.1412-1.04811.3625-0.0243-0.2682-0.22430.11350.09710.06360.0956-0.055-0.0728-0.19520.02680.0089-0.1860.06690.1823-2.751918.6514-22.6332
35.50990.53971.14913.6172-1.08233.3679-0.0247-0.2668-0.10610.194-0.10320.1716-0.1322-0.0180.1279-0.2608-0.02170.013-0.1920.10750.16127.290125.878-17.5318
42.1355-0.3316-1.20952.4427-1.1744.61520.0372-0.54420.240.5212-0.2858-0.4091-0.44830.51970.2486-0.2461-0.1323-0.1095-0.09470.06950.204816.667232.1091-10.2484
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|515 - 561}
2X-RAY DIFFRACTION2{A|562 - 620}
3X-RAY DIFFRACTION3{A|621 - 712}
4X-RAY DIFFRACTION4{A|713 - 794}

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