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- PDB-6gvj: Human Mps1 kinase domain with ordered activation loop -

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Basic information

Entry
Database: PDB / ID: 6gvj
TitleHuman Mps1 kinase domain with ordered activation loop
ComponentsDual specificity protein kinase TTK
KeywordsTRANSFERASE / MPS1 / TTK / KINASE / MITOSIS CHECKPOINT / Activation loop / activation segment
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
Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.41 Å
AuthorsRoorda, J.C. / Hiruma, Y. / Joosten, R.P. / Perrakis, A.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research722.015.008 Netherlands
Netherlands Organisation for Scientific Research723.013.003 Netherlands
CitationJournal: Proteins / Year: 2019
Title: A crystal structure of the human protein kinase Mps1 reveals an ordered conformation of the activation loop.
Authors: Roorda, J.C. / Joosten, R.P. / Perrakis, A. / Hiruma, Y.
History
DepositionJun 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 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)49,4969
Polymers48,8731
Non-polymers6238
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-22 kcal/mol
Surface area14250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.825, 102.613, 110.973
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: 48872.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTK, MPS1, MPS1L1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P33981, dual-specificity kinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.07 Å3/Da / Density % sol: 40.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Ammonium sulfate 20% (w/v) PEG8000 0.1 M MES-buffer, pH 6.5
Temp details: Room Temperature

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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: Apr 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.41→58.29 Å / Num. obs: 15900 / % possible obs: 99.7 % / Redundancy: 4.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.045 / Rrim(I) all: 0.097 / Net I/σ(I): 10.4 / Num. measured all: 72288 / Scaling rejects: 275
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.41-2.474.10.524474611560.6030.3010.6082.399.7
10.78-58.294.40.0399162090.9980.020.04424.698.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.451
Highest resolutionLowest resolution
Rotation58.29 Å2.53 Å

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Processing

Software
NameVersionClassification
REFMACrefmac_5.8.0222refinement
Aimless0.6.3data scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HMN

3hmn


Resolution: 2.41→58.29 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / Matrix type: sparse / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.188 / SU B: 16.826 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 813 5.1 %RANDOM
Rwork0.2012 15092 --
obs0.2028 15092 99.12 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 116.06 Å2 / Biso mean: 50.838 Å2 / Biso min: 29.48 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å2-0 Å2
2---0.99 Å2-0 Å2
3---2.22 Å2
Refinement stepCycle: final / Resolution: 2.41→58.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2209 0 38 30 2277
Biso mean--68.14 48.4 -
Num. residues----272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0152286
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172120
X-RAY DIFFRACTIONr_angle_refined_deg1.0181.7473080
X-RAY DIFFRACTIONr_angle_other_deg0.3531.7224984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3115270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01622.63276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15115383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.077156
X-RAY DIFFRACTIONr_chiral_restr0.0460.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212448
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02388
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
2.408-2.470.299520.2751041117093.4190.249
2.47-2.5380.292680.2851069114998.9560.249
2.538-2.6110.291640.2671030110399.1840.235
2.611-2.6910.311500.2521017106999.8130.215
2.691-2.7790.361560.231992104999.9050.195
2.779-2.8770.268490.215961101199.9010.176
2.877-2.9850.192470.20191496299.8960.169
2.985-3.1070.268550.20389595299.790.172
3.107-3.2440.228450.19984388999.8880.177
3.244-3.4020.242510.20880485899.650.186
3.402-3.5860.209370.19379984299.2870.181
3.586-3.8020.23350.17474678998.9860.164
3.802-4.0630.171290.1769972999.8630.164
4.063-4.3870.185430.1746587011000.171
4.387-4.8030.173250.16961363999.8440.17
4.803-5.3660.222230.18455658099.8280.188
5.366-6.1870.311290.23449352399.8090.23
6.187-7.5560.262320.22941245098.6670.238
7.556-10.5970.192190.16233435699.1570.171
10.597-58.2890.12740.23521522398.2060.253
Refinement TLS params.Method: refined / Origin x: 4.1323 Å / Origin y: -14.6725 Å / Origin z: -20.9672 Å
111213212223313233
T0.0134 Å2-0.002 Å2-0.0026 Å2-0.1381 Å2-0.0477 Å2--0.0404 Å2
L1.9952 °20.1551 °2-0.5108 °2-1.0127 °2-0.2138 °2--1.1372 °2
S0.0663 Å °-0.1207 Å °0.2151 Å °0.0835 Å °0.0101 Å °-0.0658 Å °0.0395 Å °-0.0032 Å °-0.0764 Å °

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