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- PDB-5ntt: Crystal structure of human Mps1 (TTK) C604Y mutant in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5ntt
TitleCrystal structure of human Mps1 (TTK) C604Y mutant in complex with NMS-P715
ComponentsDual specificity protein kinase TTK
KeywordsTRANSFERASE / Mps1 / TTK / kinase / inhibitor / NMS-P715 / mutant / C604Y
Function / homology
Function and homology information


protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization ...protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization / chromosome segregation / kinetochore / spindle / protein tyrosine kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / ATP binding / membrane / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Protein kinase Mps1 family / Tetratricopeptide-like helical domain superfamily / 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 Mps1 family / Tetratricopeptide-like helical domain superfamily / 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
Chem-SVE / Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsHiruma, Y. / Joosten, R.P. / Perrakis, A.
Funding support Netherlands, 3items
OrganizationGrant numberCountry
Netherlands Organization for Scientific Research722.015.008 Netherlands
Netherlands Organization for Scientific Research723.013.003 Netherlands
KWF Dutch Cancer Society2012-5427 Netherlands
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Understanding inhibitor resistance in Mps1 kinase through novel biophysical assays and structures.
Authors: Hiruma, Y. / Koch, A. / Hazraty, N. / Tsakou, F. / Medema, R.H. / Joosten, R.P. / Perrakis, A.
History
DepositionApr 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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: Dual specificity protein kinase TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1894
Polymers33,3881
Non-polymers8013
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint7 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.672, 112.010, 116.126
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Dual specificity protein kinase TTK / Phosphotyrosine picked threonine-protein kinase / PYT


Mass: 33388.172 Da / Num. of mol.: 1 / Mutation: C604Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTK, MPS1, MPS1L1 / Production host: Escherichia coli (E. coli) / 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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.44 Å3/Da / Density % sol: 64.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 10.5% (w/v) PEG 350 MME, 10 mM MgCl2, and 100 mM Tris/HCl
PH range: 7.5-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 20, 2017
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 2.75→41.65 Å / Num. obs: 12326 / % possible obs: 100 % / Redundancy: 5.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.067 / Rrim(I) all: 0.165 / Net I/σ(I): 9.6 / Num. measured all: 72378 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.75-2.95.81.4370.5710.6511.58100
8.7-41.655.20.0330.9980.0160.03799.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.49 Å41.65 Å
Translation5.49 Å41.65 Å

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHASER2.7.17phasing
REFMACrefmac_5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MRB

5mrb


Resolution: 2.75→41.65 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / Matrix type: sparse / SU B: 29.224 / SU ML: 0.252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.567 / ESU R Free: 0.288
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2298 577 4.7 %RANDOM
Rwork0.1992 ---
obs0.2006 11748 99.92 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 179.74 Å2 / Biso mean: 73.976 Å2 / Biso min: 42.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20 Å2
2---2.27 Å2-0 Å2
3---1.31 Å2
Refinement stepCycle: final / Resolution: 2.75→41.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 57 32 2359
Biso mean--86.38 56.46 -
Num. residues----277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192391
X-RAY DIFFRACTIONr_bond_other_d0.0010.022214
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9633238
X-RAY DIFFRACTIONr_angle_other_deg0.8682.9765176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7375277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27325.273110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99715439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.539157
X-RAY DIFFRACTIONr_chiral_restr0.0690.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212567
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02439
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
2.75-2.8210.283410.33586190399.8890.326
2.821-2.8990.27380.3248178551000.305
2.899-2.9830.269420.2968028441000.271
2.983-3.0740.318560.3137778331000.286
3.074-3.1750.198270.2677778041000.238
3.175-3.2860.247420.2497247661000.217
3.286-3.410.292390.23272776799.870.2
3.41-3.5490.252300.2366847141000.209
3.549-3.7060.266260.2046787041000.181
3.706-3.8870.266220.1846366581000.164
3.887-4.0970.22350.1645906251000.148
4.097-4.3440.204320.1535806121000.139
4.344-4.6430.163300.14254457599.8260.131
4.643-5.0140.162260.15249652399.8090.134
5.014-5.490.123140.1714955091000.156
5.49-6.1350.211190.24204391000.179
6.135-7.0770.268220.2013834051000.183
7.077-8.6510.241120.1583353471000.146
8.651-12.1650.234180.1426027999.6420.136
12.165-80.6190.26660.23816217397.110.241
Refinement TLS params.Method: refined / Origin x: -4.3213 Å / Origin y: -21.4849 Å / Origin z: -17.1382 Å
111213212223313233
T0.0299 Å2-0.0013 Å2-0.0357 Å2-0.0874 Å2-0.0431 Å2--0.1902 Å2
L2.9584 °21.0997 °2-0.5096 °2-2.2985 °20.183 °2--1.2089 °2
S0.0761 Å °-0.4482 Å °-0.0769 Å °0.2011 Å °-0.1254 Å °-0.0151 Å °0.0916 Å °0.0243 Å °0.0493 Å °

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