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- PDB-4b94: Crystal structure of human Mps1 TPR domain -

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Basic information

Entry
Database: PDB / ID: 4b94
TitleCrystal structure of human Mps1 TPR domain
ComponentsDUAL SPECIFICITY PROTEIN KINASE TTK
KeywordsTRANSFERASE / KINETOCHORE / MITOSIS
Function / homology
Function and homology information


protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / repair of mitotic kinetochore microtubule attachment defect / 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 ...protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / repair of mitotic kinetochore microtubule attachment defect / 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
MALONATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsLittler, D. / von Castelmur, E. / De Marco, V. / Perrakis, A.
CitationJournal: J.Cell Biol. / Year: 2013
Title: A Tpr Domain-Containing N-Terminal Module of Mps1 is Required for its Kinetochore Localization by Aurora B.
Authors: Nijenhuis, W. / von Castelmur, E. / Littler, D. / De Marco, V. / Tromer, E. / Vleugel, M. / van Osch, M.H. / Snel, B. / Perrakis, A. / Kops, G.J.
History
DepositionAug 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Dec 13, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,19221
Polymers81,2734
Non-polymers1,92017
Water4,179232
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A: DUAL SPECIFICITY PROTEIN KINASE TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6974
Polymers20,3181
Non-polymers3783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DUAL SPECIFICITY PROTEIN KINASE TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0418
Polymers20,3181
Non-polymers7237
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DUAL SPECIFICITY PROTEIN KINASE TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6674
Polymers20,3181
Non-polymers3483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DUAL SPECIFICITY PROTEIN KINASE TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7895
Polymers20,3181
Non-polymers4714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.920, 80.137, 142.212
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
DUAL SPECIFICITY PROTEIN KINASE TTK / MPS1 / PHOSPHOTYROSINE PICKED THREONINE-PROTEIN KINASE / PYT


Mass: 20318.135 Da / Num. of mol.: 4 / Fragment: TPR DOMAIN, RESIDUES 62-239
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETNKI-HIS-3C-LIC-KAN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): T1R / References: UniProt: P33981, dual-specificity kinase

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Non-polymers , 6 types, 249 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 3.6 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growpH: 5 / Details: 0.1M MIB PH 5.0, 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9793
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→40.77 Å / Num. obs: 46492 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 39.53 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.8 / % possible all: 92.7

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.2→40.8 Å / Cor.coef. Fo:Fc: 0.9541 / Cor.coef. Fo:Fc free: 0.9514 / SU R Cruickshank DPI: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.16 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.132 / Details: RESIDUES 200-239 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.1858 2362 5.08 %RANDOM
Rwork0.17 ---
obs0.1708 46492 98.68 %-
Displacement parametersBiso mean: 50.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.5909 Å20 Å20 Å2
2--0.691 Å20 Å2
3----3.2818 Å2
Refine analyzeLuzzati coordinate error obs: 0.276 Å
Refinement stepCycle: LAST / Resolution: 2.2→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4446 0 127 232 4805
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014670HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.976241HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1761SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes142HARMONIC2
X-RAY DIFFRACTIONt_gen_planes643HARMONIC5
X-RAY DIFFRACTIONt_it4670HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.71
X-RAY DIFFRACTIONt_other_torsion18.55
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion560SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5372SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2292 147 4.77 %
Rwork0.2029 2935 -
all0.2042 3082 -
obs--98.68 %
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)
13.7515-0.17270.53211.4620.32281.4053-0.0889-0.2320.35860.1889-0.0372-0.0165-0.1418-0.0760.1261-0.2274-0.0092-0.0075-0.12970.0043-0.242726.195866.893910.8361
21.8994-0.1799-0.71564.90710.04951.39080.0654-0.40410.09530.73870.0065-0.63820.12560.2879-0.0718-0.0960.0069-0.1008-0.2483-0.0511-0.256746.573864.481242.9701
35.37430.51630.11162.40650.49841.6512-0.08061.00110.7046-0.30840.13990.0176-0.1918-0.1811-0.0594-0.3209-0.01460.03150.00630.1643-0.266942.097867.0262-7.861
41.7318-0.7092-0.43563.2788-0.41591.3162-0.02640.13040.0046-0.1877-0.1203-0.34250.09490.10390.1466-0.19270.0040.0263-0.25570.0206-0.22545.891948.676324.4479
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 2-199
2X-RAY DIFFRACTION2CHAIN B AND RESID 2-195
3X-RAY DIFFRACTION3CHAIN C AND RESID 2-195
4X-RAY DIFFRACTION4CHAIN D AND RESID 2-195

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