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- PDB-5ljj: Crystal structure of human Mps1 (TTK) in complex with Reversine -

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Basic information

Entry
Database: PDB / ID: 5ljj
TitleCrystal structure of human Mps1 (TTK) in complex with Reversine
ComponentsDual specificity protein kinase TTK
KeywordsTRANSFERASE / Mps1 / Reversine / TTK / kinase / mitosis checkpoint
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-AD5 / Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsHiruma, Y. / Joosten, R.P. / Perrakis, A.
Funding support Netherlands, 3items
OrganizationGrant numberCountry
NWO722.015.008 Netherlands
NWO723.013.003 Netherlands
KWF2012-5427 Netherlands
CitationJournal: Proteins / Year: 2016
Title: Structural basis of reversine selectivity in inhibiting Mps1 more potently than aurora B kinase.
Authors: Hiruma, Y. / Koch, A. / Dharadhar, S. / Joosten, R.P. / Perrakis, A.
History
DepositionJul 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Nov 30, 2016Group: Database references
Revision 1.3Aug 16, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.4Nov 2, 2022Group: Database references / Structure summary / Category: chem_comp / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)36,6313
Polymers36,1751
Non-polymers4562
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint2 kcal/mol
Surface area14150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.852, 109.570, 113.209
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: 36175.289 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 BL21(DE3) (bacteria) / References: UniProt: P33981, dual-specificity kinase
#2: Chemical ChemComp-AD5 / N~6~-cyclohexyl-N~2~-(4-morpholin-4-ylphenyl)-9H-purine-2,6-diamine / Reversine / Reversine


Mass: 393.485 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O / Comment: antagonist*YM
#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

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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: 3.04 Å3/Da / Density % sol: 59.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein sollution: 200 uM (7.2 mg/mL) mps1, 250 uM reversine. Reservoir solution: 7.6% (w/v) PEG 350 MME, 0.5 mM MgCl2, and 100 mM Tris/HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.96771 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 16, 2016
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96771 Å / Relative weight: 1
ReflectionResolution: 3→41.01 Å / Num. obs: 9005 / % possible obs: 99 % / Redundancy: 4.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.051 / Rrim(I) all: 0.115 / Net I/σ(I): 10.5 / Num. measured all: 40889
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3-3.1840.932578214300.7850.4991.0651.398.1
9-41.014.30.02515833640.9990.0130.02942.296.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.41 Å41.01 Å
Translation6.41 Å41.01 Å

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Processing

Software
NameVersionClassification
REFMACrefmac_5.8.0155refinement
Aimless0.5.25data scaling
PHASER2.6.1phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3hmn

3hmn


Resolution: 3→41.01 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / Matrix type: sparse / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.19 / SU B: 68.042 / SU ML: 0.462 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2678 877 9.7 %RANDOM
Rwork0.2237 8127 --
obs0.2281 8127 98.43 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 188.68 Å2 / Biso mean: 108.599 Å2 / Biso min: 75.38 Å2
Baniso -1Baniso -2Baniso -3
1--3.3 Å2-0 Å2-0 Å2
2--10.56 Å20 Å2
3----7.26 Å2
Refinement stepCycle: final / Resolution: 3→41.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2161 0 33 0 2194
Biso mean--83.85 --
Num. residues----264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192245
X-RAY DIFFRACTIONr_bond_other_d0.0010.022165
X-RAY DIFFRACTIONr_angle_refined_deg1.0711.9583032
X-RAY DIFFRACTIONr_angle_other_deg0.8472.9815006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6575261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77925.577104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01615417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.492156
X-RAY DIFFRACTIONr_chiral_restr0.0650.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212483
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02494
X-RAY DIFFRACTIONr_mcbond_it0.7647.5251053
X-RAY DIFFRACTIONr_mcbond_other0.7647.5231052
X-RAY DIFFRACTIONr_mcangle_it1.4111.2771311
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
3-3.0780.494580.44358767395.840.429
3.078-3.1620.338600.42956763399.0520.397
3.162-3.2540.441620.36856462899.6820.326
3.254-3.3540.422600.33355261699.3510.295
3.354-3.4640.293780.3551259399.4940.32
3.464-3.5850.357520.26651557398.9530.229
3.585-3.720.299570.25449755799.4610.22
3.72-3.8710.229520.23547453199.0580.204
3.871-4.0430.227370.17748152199.4240.152
4.043-4.240.274460.1843748799.1790.161
4.24-4.4690.192340.16643146999.1470.149
4.469-4.7390.221550.16639545598.9010.149
4.739-5.0640.237340.16639143298.380.149
5.064-5.4680.251390.19434038797.9330.175
5.468-5.9870.317380.22330735996.10.203
5.987-6.6890.28370.21329834098.5290.193
6.689-7.7150.291170.16527529798.3160.156
7.715-9.4260.141230.15822725797.2760.162
9.426-13.2360.184160.15518320796.1350.172
13.236-78.7330.263220.3169413387.2180.312
Refinement TLS params.Method: refined / Origin x: -30.644 Å / Origin y: -16.3159 Å / Origin z: -21.434 Å
111213212223313233
T0.0824 Å20.0352 Å20.0023 Å2-0.5321 Å20.0032 Å2--0.0902 Å2
L4.3504 °21.1283 °2-2.0047 °2-1.24 °2-0.0587 °2--4.0013 °2
S0.0905 Å °0.3023 Å °0.5439 Å °-0.1882 Å °-0.0021 Å °0.078 Å °-0.446 Å °-0.0313 Å °-0.0883 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A515 - 795
2X-RAY DIFFRACTION1A900

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