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- PDB-4h7y: Crystal structure of the tetratricopeptide repeat (TPR) motif of ... -

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Basic information

Entry
Database: PDB / ID: 4h7y
TitleCrystal structure of the tetratricopeptide repeat (TPR) motif of human dual specificity protein kinase Mps1
ComponentsDual specificity protein kinase TTK
KeywordsTRANSFERASE / Mitotic checkpoint kinase / Chromosome instability / Cancer / Tetratricopeptide repeat (TPR) motif / Mitotic 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 / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / ATP binding / identical protein binding / membrane / nucleus / cytoplasm
Similarity search - Function
Protein kinase Mps1 family / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / 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 kinase Mps1 family / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / 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 / Mainly Alpha
Similarity search - Domain/homology
Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsBolanos-Garcia, V.M. / Chirgadze, D.Y. / Blundell, T.L.
CitationJournal: Biochem.J. / Year: 2012
Title: Structural and functional insights into the role of the N-terminal Mps1 TPR domain in the SAC (spindle assembly checkpoint).
Authors: Thebault, P. / Chirgadze, D.Y. / Dou, Z. / Blundell, T.L. / Elowe, S. / Bolanos-Garcia, V.M.
History
DepositionSep 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein kinase TTK
B: Dual specificity protein kinase TTK
C: Dual specificity protein kinase TTK
D: Dual specificity protein kinase TTK


Theoretical massNumber of molelcules
Total (without water)72,7484
Polymers72,7484
Non-polymers00
Water9,062503
1
A: Dual specificity protein kinase TTK


Theoretical massNumber of molelcules
Total (without water)18,1871
Polymers18,1871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dual specificity protein kinase TTK


Theoretical massNumber of molelcules
Total (without water)18,1871
Polymers18,1871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dual specificity protein kinase TTK


Theoretical massNumber of molelcules
Total (without water)18,1871
Polymers18,1871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Dual specificity protein kinase TTK


Theoretical massNumber of molelcules
Total (without water)18,1871
Polymers18,1871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.502, 80.250, 141.278
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 18187.055 Da / Num. of mol.: 4 / Fragment: TPR domain (UNP residues 55-210)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: MPS1, MPS1L1, NCBI Reference Sequence NM_003318.4, TTK
Plasmid: pGST-TPR-Mps1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33981, dual-specificity kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6
Details: 20% PEG 3350, 100 mM MES, 250 mM KCl, pH 6.0, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→28.5 Å / Num. all: 81073 / Num. obs: 80100 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 20.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.572 / % possible all: 98.6

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Processing

Software
NameVersionClassification
GDAdata collection
PHENIX(phenix.refine: 1.7.3_928)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→28.5 Å / SU ML: 0.26 / σ(F): 0 / Phase error: 24.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 1926 2.4 %random
Rwork0.1986 ---
all0.1992 81073 --
obs0.1992 80100 98.6 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.644 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.2132 Å20 Å20 Å2
2--6.3327 Å2-0 Å2
3---0.8805 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4444 0 0 503 4947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064558
X-RAY DIFFRACTIONf_angle_d0.9366143
X-RAY DIFFRACTIONf_dihedral_angle_d15.2111783
X-RAY DIFFRACTIONf_chiral_restr0.057679
X-RAY DIFFRACTIONf_plane_restr0.005807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.84510.38021210.31514878X-RAY DIFFRACTION84
1.8451-1.89490.36051320.27845081X-RAY DIFFRACTION88
1.8949-1.95070.28111250.25885256X-RAY DIFFRACTION90
1.9507-2.01360.26231290.23535408X-RAY DIFFRACTION93
2.0136-2.08560.31371360.22595552X-RAY DIFFRACTION95
2.0856-2.16910.26461360.20755641X-RAY DIFFRACTION97
2.1691-2.26770.24231410.20575662X-RAY DIFFRACTION97
2.2677-2.38720.27541420.19925686X-RAY DIFFRACTION97
2.3872-2.53670.23021420.1965807X-RAY DIFFRACTION99
2.5367-2.73240.25721390.19275817X-RAY DIFFRACTION99
2.7324-3.00710.20981450.20095845X-RAY DIFFRACTION99
3.0071-3.44170.21431410.1935826X-RAY DIFFRACTION98
3.4417-4.33370.17661480.17365809X-RAY DIFFRACTION97
4.3337-28.51410.21171490.1945906X-RAY DIFFRACTION95

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