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- PDB-5o91: Crystal structure of human Mps1 (TTK) C604W mutant in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5o91
TitleCrystal structure of human Mps1 (TTK) C604W mutant in complex with Cpd-5
ComponentsDual specificity protein kinase TTK
KeywordsTRANSFERASE / Mps1 / TTK / kinase / inhibitor / Cpd-5 / mutant / C604W
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-C5N / Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 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
DepositionJun 15, 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 1.2Aug 9, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.3Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 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

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Assembly

Deposited unit
A: Dual specificity protein kinase TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8413
Polymers36,1981
Non-polymers6432
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint4 kcal/mol
Surface area14300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.670, 111.889, 116.800
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: 36198.320 Da / Num. of mol.: 1 / Mutation: C604W
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-C5N / ~{N}-(2,6-diethylphenyl)-8-[[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino]-1-methyl-4,5-dihydropyrazolo[4,3-h]quinazoline-3-carboxamide


Mass: 580.723 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H40N8O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.19 Å3/Da / Density % sol: 61.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 12.3% (w/v) PEG 350 MME. 1 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: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 3.2→41.76 Å / Num. obs: 7947 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.985 / Rmerge(I) obs: 0.282 / Rpim(I) all: 0.12 / Rrim(I) all: 0.307 / Net I/σ(I): 6 / Num. measured all: 51034 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
3.2-3.426.31.7840.5380.7721.947100
9.05-41.766.20.0650.9960.0280.07199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.47 Å41.76 Å
Translation5.47 Å41.76 Å

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHASER2.7.17phasing
REFMACrefmac_5.8.0173refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MRB

5mrb


Resolution: 3.2→41.76 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.888 / Matrix type: sparse / SU B: 52.111 / SU ML: 0.377 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0 / ESU R Free: 0.453
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2544 437 5.5 %RANDOM
Rwork0.2121 ---
obs0.2144 7510 99.91 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 156.48 Å2 / Biso mean: 78.274 Å2 / Biso min: 24.64 Å2
Baniso -1Baniso -2Baniso -3
1--3.31 Å2-0 Å20 Å2
2---0.92 Å2-0 Å2
3---4.23 Å2
Refinement stepCycle: final / Resolution: 3.2→41.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 47 10 2242
Biso mean--93.09 34.92 -
Num. residues----266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192287
X-RAY DIFFRACTIONr_bond_other_d0.0020.022120
X-RAY DIFFRACTIONr_angle_refined_deg1.1891.9553094
X-RAY DIFFRACTIONr_angle_other_deg0.8482.9744952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1725263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.07225.429105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07315420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.881156
X-RAY DIFFRACTIONr_chiral_restr0.0670.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212460
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02425
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
3.2-3.2830.484270.3795525791000.379
3.283-3.3730.376330.3735235561000.37
3.373-3.470.236190.3235215401000.308
3.47-3.5770.308280.2945085361000.278
3.577-3.6940.316270.2754935201000.253
3.694-3.8240.336240.2194734971000.195
3.824-3.9680.265300.2124424721000.187
3.968-4.1290.229360.1874424781000.167
4.129-4.3120.18200.1824194391000.163
4.312-4.5220.195230.1654074301000.15
4.522-4.7660.237270.1513864131000.132
4.766-5.0540.161240.1673693931000.141
5.054-5.4010.207140.1843483621000.161
5.401-5.8320.299200.19332835099.4290.171
5.832-6.3850.304140.2393003141000.214
6.385-7.1330.284230.2042652881000.183
7.133-8.2260.203250.1522372621000.139
8.226-10.0490.246160.1522082241000.143
10.049-14.1030.09720.1491831851000.141
14.103-80.7980.35350.33910611695.690.318
Refinement TLS params.Method: refined / Origin x: -4.4338 Å / Origin y: -22.2726 Å / Origin z: -17.4299 Å
111213212223313233
T0.0317 Å20.0329 Å2-0.0224 Å2-0.1077 Å2-0.0467 Å2--0.0427 Å2
L3.7106 °21.342 °2-0.8224 °2-2.9968 °20.1504 °2--1.9089 °2
S0.0288 Å °-0.3893 Å °0.0085 Å °0.2103 Å °-0.0308 Å °0.0399 Å °0.0506 Å °-0.0102 Å °0.002 Å °

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