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- PDB-4h7x: Crystal structure of the tetratricopeptide repeat (TPR) motif of ... -

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Basic information

Entry
Database: PDB / ID: 4h7x
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 / 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 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
LEAD (II) ION / Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
B: Dual specificity protein kinase TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5813
Polymers36,3742
Non-polymers2071
Water93752
1
A: Dual specificity protein kinase TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3942
Polymers18,1871
Non-polymers2071
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
Unit cell
Length a, b, c (Å)79.487, 79.487, 137.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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.: 2 / 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: Chemical ChemComp-PB / LEAD (II) ION / Lead


Mass: 207.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pb
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.99 Å3/Da / Density % sol: 58.86 %
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: I04 / Wavelength: 0.9497 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9497 Å / Relative weight: 1
ReflectionResolution: 2.6→39.7 Å / Num. all: 14021 / Num. obs: 14021 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.156 / Rsym value: 0.156 / Net I/σ(I): 7.2
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.599 / % possible all: 99.9

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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
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→39.7 Å / SU ML: 0.29 / σ(F): 0 / Phase error: 21.72 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1399 9.98 %random
Rwork0.1928 ---
all0.1975 14021 --
obs0.1975 14021 99.9 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.41 Å2 / ksol: 0.365 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.808 Å2-0 Å20 Å2
2---1.808 Å20 Å2
3---3.616 Å2
Refinement stepCycle: LAST / Resolution: 2.6→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2186 0 1 52 2239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092222
X-RAY DIFFRACTIONf_angle_d1.0632997
X-RAY DIFFRACTIONf_dihedral_angle_d15.828849
X-RAY DIFFRACTIONf_chiral_restr0.066334
X-RAY DIFFRACTIONf_plane_restr0.004395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.606-2.69910.30721340.21191218X-RAY DIFFRACTION97
2.6991-2.80720.26881360.21081218X-RAY DIFFRACTION98
2.8072-2.93490.30491360.21121208X-RAY DIFFRACTION99
2.9349-3.08960.2981380.21461242X-RAY DIFFRACTION99
3.0896-3.28310.27371390.21591259X-RAY DIFFRACTION100
3.2831-3.53640.23791390.19281260X-RAY DIFFRACTION100
3.5364-3.8920.22871380.18131255X-RAY DIFFRACTION100
3.892-4.45450.20511410.16251274X-RAY DIFFRACTION100
4.4545-5.60970.21771460.17991306X-RAY DIFFRACTION100
5.6097-39.74990.21461520.20441382X-RAY DIFFRACTION99

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