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- PDB-5ap7: Naturally Occurring Mutations in the MPS1 Gene Predispose Cells t... -

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Basic information

Entry
Database: PDB / ID: 5ap7
TitleNaturally Occurring Mutations in the MPS1 Gene Predispose Cells to Kinase Inhibitor Drug Resistance.
ComponentsMONOPOLAR SPINDLE KINASE 1
KeywordsTRANSFERASE / MPS1 / MITOSIS
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-SVE / Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsGurden, M.D. / Westwood, I.M. / Faisal, A. / Naud, S. / Cheung, K.M. / McAndrew, C. / Wood, A. / Schmitt, J. / Boxall, K. / Mak, G. ...Gurden, M.D. / Westwood, I.M. / Faisal, A. / Naud, S. / Cheung, K.M. / McAndrew, C. / Wood, A. / Schmitt, J. / Boxall, K. / Mak, G. / Workman, P. / Burke, R. / Hoelder, S. / Blagg, J. / van Montfort, R. / 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MONOPOLAR SPINDLE KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2648
Polymers36,1981
Non-polymers1,0657
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.720, 111.970, 116.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 36198.320 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 519-808 / Mutation: YES
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
#2: Chemical ChemComp-SVE / N-(2,6-DIETHYLPHENYL)-1-METHYL-8-({4-[(1-METHYLPIPERIDIN-4-YL)CARBAMOYL]-2-(TRIFLUOROMETHOXY)PHENYL}AMINO)-4,5-DIHYDRO-1H-PYRAZOLO[4,3-H]QUINAZOLINE-3-CARBOXAMIDE


Mass: 676.731 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H39F3N8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 604 TO TRP
Sequence detailsTHE SEQUENCE INCLUDING HEXAHISTIDINE TAG IS AS DESCRIBED IN NAT. CHEM. BIOL. 2010, 6, 259-368 WITH ...THE SEQUENCE INCLUDING HEXAHISTIDINE TAG IS AS DESCRIBED IN NAT. CHEM. BIOL. 2010, 6, 259-368 WITH AN ADDITIONAL MUTATION C604W

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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: 3.18 Å3/Da / Density % sol: 61.28 % / Description: NONE
Crystal growpH: 8 / Details: 0.1M TRIS, PH 8.0, 0.2M MGCL2, 20% (W/ V) PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Sep 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.45→41.66 Å / Num. obs: 17195 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 73.78 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.4
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.46 / Mean I/σ(I) obs: 1.1 / % possible all: 99.9

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Processing

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

4c4j


Resolution: 2.45→41.66 Å / Cor.coef. Fo:Fc: 0.9474 / Cor.coef. Fo:Fc free: 0.9291 / SU R Cruickshank DPI: 0.231 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.228 / SU Rfree Blow DPI: 0.201 / SU Rfree Cruickshank DPI: 0.204
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 873 5.08 %RANDOM
Rwork0.186 ---
obs0.1882 17192 99.24 %-
Displacement parametersBiso mean: 72 Å2
Baniso -1Baniso -2Baniso -3
1-7.1388 Å20 Å20 Å2
2---2.7217 Å20 Å2
3----4.4171 Å2
Refine analyzeLuzzati coordinate error obs: 0.336 Å
Refinement stepCycle: LAST / Resolution: 2.45→41.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2060 0 73 41 2174
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012182HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.112955HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d743SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes52HARMONIC2
X-RAY DIFFRACTIONt_gen_planes338HARMONIC5
X-RAY DIFFRACTIONt_it2182HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion19.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion285SEMIHARMONIC5
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_contact2383SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.6 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2602 164 5.99 %
Rwork0.2318 2574 -
all0.2336 2738 -
obs--99.24 %
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)
15.54222.77670.5478.05962.90133.8883-0.0296-0.20560.32440.21560.1315-0.5282-0.31950.3484-0.1019-0.12920.02010.029-0.3-0.10140.23259.4734-5.3428-19.4139
23.29671.4959-2.91043.222.79930.15520.059-0.01830.0055-0.02330.254-0.3774-0.2480.5026-0.313-0.06230.0781-0.0533-0.1331-0.14910.134810.5382-11.931-22.5823
34.19980.8888-2.83790.97832.50430.417-0.01540.1239-0.0908-0.08950.0650.04230.03780.0685-0.0496-0.15690.02540.0155-0.1217-0.10020.21058.9558-26.6313-26.2555
46.61550.9818-0.99755.25742.75974.33640.06190.18520.17040.13420.1208-0.4277-0.0556-0.1543-0.1827-0.08770.0663-0.0541-0.22030.00770.0564-0.4069-14.9283-22.1653
55.60071.85911.69311.2681-1.78461.1513-0.03530.1623-0.10710.10460.06220.0384-0.0906-0.1542-0.0268-0.18490.0138-0.0417-0.1081-0.07840.1378-13.6418-23.5467-22.7977
67.16012.8908-2.77132.61021.76314.52690.0729-0.1129-0.03770.0452-0.0097-0.0079-0.1244-0.0541-0.0632-0.13770.02060.0033-0.0659-0.07220.0619-5.7323-20.9889-19.2934
70.4823-1.4808-2.68971.0425-1.07121.39820.0401-0.3921-0.21060.09960.0454-0.08430.07990.2224-0.0854-0.1511-0.0621-0.0936-0.02620.04550.1969-0.1671-30.4382-12.3537
83.6836-0.6945-0.54461.15030.68413.6069-0.0513-0.5442-0.54420.5424-0.15680.15270.4794-0.49350.2081-0.131-0.12060.0424-0.06250.05780.078-15.6511-31.8058-7.9045
90.20781.9030.98910.67292.64550.2972-0.0171-0.0374-0.069-0.0038-0.08020.0408-0.1624-0.140.0973-0.2275-0.04710.0192-0.0829-0.1520.2735-22.3453-28.7183-23.7106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|509 - 544}
2X-RAY DIFFRACTION2{A|545 - 561}
3X-RAY DIFFRACTION3{A|562 - 578}
4X-RAY DIFFRACTION4{A|579 - 620}
5X-RAY DIFFRACTION5{A|621 - 641}
6X-RAY DIFFRACTION6{A|642 - 662}
7X-RAY DIFFRACTION7{A|663 - 712}
8X-RAY DIFFRACTION8{A|713 - 781}
9X-RAY DIFFRACTION9{A|782 - 794}

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