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- PDB-3cek: Crystal structure of human dual specificity protein kinase (TTK) -

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Basic information

Entry
Database: PDB / ID: 3cek
TitleCrystal structure of human dual specificity protein kinase (TTK)
ComponentsDual specificity protein kinase TTK
KeywordsTRANSFERASE / TTK / hMPS1 / PYT / ESK / kinase / dual specificity / phosphotyrosine picked threonine kinase / SGC / Structural Genomics Consortium / ATP-binding / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Tyrosine-protein kinase
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 / spindle / kinetochore / 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-7PE / Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsFilippakopoulos, P. / Soundararajan, M. / Keates, T. / Elkins, J.M. / King, O. / Fedorov, O. / Picaud, S.S. / Pike, A.C.W. / Roos, A. / Pilka, E. ...Filippakopoulos, P. / Soundararajan, M. / Keates, T. / Elkins, J.M. / King, O. / Fedorov, O. / Picaud, S.S. / Pike, A.C.W. / Roos, A. / Pilka, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Chem.Biol. / Year: 2010
Title: Small-molecule kinase inhibitors provide insight into Mps1 cell cycle function.
Authors: Kwiatkowski, N. / Jelluma, N. / Filippakopoulos, P. / Soundararajan, M. / Manak, M.S. / Kwon, M. / Choi, H.G. / Sim, T. / Deveraux, Q.L. / Rottmann, S. / Pellman, D. / Shah, J.V. / Kops, G.J. ...Authors: Kwiatkowski, N. / Jelluma, N. / Filippakopoulos, P. / Soundararajan, M. / Manak, M.S. / Kwon, M. / Choi, H.G. / Sim, T. / Deveraux, Q.L. / Rottmann, S. / Pellman, D. / Shah, J.V. / Kops, G.J. / Knapp, S. / Gray, N.S.
History
DepositionFeb 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Dual specificity protein kinase TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7363
Polymers36,1151
Non-polymers6212
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Dual specificity protein kinase TTK
hetero molecules

A: Dual specificity protein kinase TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4726
Polymers72,2312
Non-polymers1,2424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1970 Å2
ΔGint-15.7 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.846, 107.467, 111.872
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-938-

HOH

DetailsAUTHORS STATE THAT THE GEL FILTRATION SUGGESTS A MONOMERIC ASSEMBLY OF THE BIOLOGICAL UNIT.

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Components

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


Mass: 36115.258 Da / Num. of mol.: 1 / Fragment: Protein kinase domain: Residues 519-808
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTK, MPS1L1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: P33981, dual-specificity kinase
#2: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT / Polyethylene glycol


Mass: 310.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 55% PEG 300, 0.25M NaCl, Na/K Phosphate pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97912 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.3→40.456 Å / Num. all: 19092 / Num. obs: 19054 / % possible obs: 99.8 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 17.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2722 / % possible all: 99.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å32.9 Å
Translation2.5 Å32.9 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2QKR, 2H9V, 2F2U, 2EUE

2qkr

2h9v

2f2u

2eue
PDB Unreleased entry


Resolution: 2.3→34 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.479 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 980 5.1 %RANDOM
Rwork0.184 ---
all0.188 19053 --
obs0.188 19053 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.156 Å2
Baniso -1Baniso -2Baniso -3
1--2.35 Å20 Å20 Å2
2--2.8 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 32 69 2132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222106
X-RAY DIFFRACTIONr_bond_other_d0.0020.021426
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9782841
X-RAY DIFFRACTIONr_angle_other_deg0.9463.0043450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4655253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.33925.38591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09715368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.939155
X-RAY DIFFRACTIONr_chiral_restr0.0910.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212267
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02382
X-RAY DIFFRACTIONr_mcbond_it2.26631278
X-RAY DIFFRACTIONr_mcbond_other0.5923510
X-RAY DIFFRACTIONr_mcangle_it3.77152067
X-RAY DIFFRACTIONr_scbond_it6.1848828
X-RAY DIFFRACTIONr_scangle_it8.40811774
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 91 -
Rwork0.239 1263 -
all-1354 -
obs--97.97 %
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)
17.09812.0405-1.18838.3594-1.62546.52330.0762-0.5597-0.53080.67290.0365-0.7990.37910.4265-0.1127-0.00380.00070.00230.1406-0.009-0.079811.249324.045751.6312
26.7695-0.6564-4.15881.88080.22779.5431-0.16-0.1598-0.50420.27040.0084-0.2930.7018-0.02720.1516-0.1365-0.0437-0.0033-0.02090.0616-0.1410.607121.573245.1626
35.47181.47181.72961.56020.51371.08730.096-0.6673-0.09210.1726-0.12020.15960.023-0.10020.0242-0.11880.00090.0089-0.09750.0277-0.1603-2.727521.400536.8064
49.08835.3775-1.72955.407-5.29588.5324-0.4877-0.4713-0.9578-0.33350.5562-1.15171.49020.4881-0.06850.0004-0.0657-0.00170.0865-0.03020.03122.279816.665431.9893
54.0194-1.26251.73787.7003-0.1764.17580.0778-0.1217-0.6932-0.1412-0.1469-0.16320.70270.48410.0691-0.1330.0112-0.071-0.1790.02230.0113-9.42946.220626.6278
69.746-2.0028-1.0341.6188-2.50826.24110.27560.2497-0.032-0.0147-0.23160.04720.4841-0.0201-0.0440.07250.0301-0.0219-0.1045-0.01470.0751-9.468-3.072121.5845
72.8507-2.0049-0.11795.8861-0.40273.4244-0.01490.237-0.6307-0.0349-0.02780.61910.2909-0.67090.0427-0.2135-0.0697-0.0757-0.09070.008-0.0036-20.469212.968725.3237
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA515 - 53320 - 38
2X-RAY DIFFRACTION2AA534 - 56339 - 68
3X-RAY DIFFRACTION3AA564 - 66169 - 166
4X-RAY DIFFRACTION4AA662 - 686167 - 191
5X-RAY DIFFRACTION5AA687 - 739192 - 244
6X-RAY DIFFRACTION6AA740 - 753245 - 258
7X-RAY DIFFRACTION7AA754 - 794259 - 299

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