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- PDB-6jkk: Crystal structure of BubR1 kinase domain -

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Basic information

Entry
Database: PDB / ID: 6jkk
TitleCrystal structure of BubR1 kinase domain
ComponentsMitotic checkpoint control protein kinase BUB1
KeywordsTRANSFERASE / Kinase / Mitotic checkpoint
Function / homology
Function and homology information


male meiosis sister chromatid cohesion / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / regulation of mitotic sister chromatid separation / synaptonemal complex organization / APC-Cdc20 mediated degradation of Nek2A / female meiosis sister chromatid cohesion / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / meiotic sister chromatid cohesion, centromeric / regulation of exit from mitosis ...male meiosis sister chromatid cohesion / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / regulation of mitotic sister chromatid separation / synaptonemal complex organization / APC-Cdc20 mediated degradation of Nek2A / female meiosis sister chromatid cohesion / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / meiotic sister chromatid cohesion, centromeric / regulation of exit from mitosis / mitotic spindle assembly checkpoint signaling / cellular response to starvation / heterochromatin formation / kinetochore / protein kinase activity / protein-containing complex / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Mad3/Bub1 homology region 1 / Mitotic spindle checkpoint protein Bub1/Mad3 / Mad3/BUB1 homology region 1 / BUB1 N-terminal domain profile. / Mad3/BUB1 hoMad3/BUB1 homology region 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 ...Mad3/Bub1 homology region 1 / Mitotic spindle checkpoint protein Bub1/Mad3 / Mad3/BUB1 homology region 1 / BUB1 N-terminal domain profile. / Mad3/BUB1 hoMad3/BUB1 homology region 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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Bub1-related kinase / Mitotic checkpoint control protein kinase BUB1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLin, L. / Ye, S. / Huang, Y. / Liu, X. / Zhang, R. / Yao, X.
CitationJournal: Cell Res. / Year: 2019
Title: BubR1 phosphorylates CENP-E as a switch enabling the transition from lateral association to end-on capture of spindle microtubules.
Authors: Huang, Y. / Lin, L. / Liu, X. / Ye, S. / Yao, P.Y. / Wang, W. / Yang, F. / Gao, X. / Li, J. / Zhang, Y. / Zhang, J. / Yang, Z. / Liu, X. / Yang, Z. / Zang, J. / Teng, M. / Wang, Z. / Ruan, K. ...Authors: Huang, Y. / Lin, L. / Liu, X. / Ye, S. / Yao, P.Y. / Wang, W. / Yang, F. / Gao, X. / Li, J. / Zhang, Y. / Zhang, J. / Yang, Z. / Liu, X. / Yang, Z. / Zang, J. / Teng, M. / Wang, Z. / Ruan, K. / Ding, X. / Li, L. / Cleveland, D.W. / Zhang, R. / Yao, X.
History
DepositionMar 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: 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: Mitotic checkpoint control protein kinase BUB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8023
Polymers39,6041
Non-polymers1982
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-0 kcal/mol
Surface area16090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.221, 61.617, 94.054
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mitotic checkpoint control protein kinase BUB1 / Mitotic checkpoint serine/threonine-protein kinase BUB1 beta


Mass: 39603.859 Da / Num. of mol.: 1 / Fragment: Protein kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: BubR1, Bub1, CG7838 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76755, UniProt: A1Z6I7*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 4% PEG 3000, 0.1M Bis-tris propane pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 29503 / % possible obs: 98 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.071 / Χ2: 1.018 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.85-1.893.40.6113360.989182
1.89-1.9240.52914850.999189.7
1.92-1.974.60.42515270.974193.8
1.97-2.015.60.35116400.968199.6
2.01-2.066.80.29316461.0021100
2.06-2.126.90.25416561.0151100
2.12-2.186.90.21116551.0051100
2.18-2.2570.18816321.0181100
2.25-2.337.10.16916561.0031100
2.33-2.4270.14516560.9781100
2.42-2.537.10.12916670.9951100
2.53-2.677.10.10816791.0111100
2.67-2.847.10.08616751.0231100
2.84-3.057.10.07116681.0541100
3.05-3.367.10.04916841.0671100
3.36-3.857.10.03917051.0011100
3.85-4.8570.03817151.057199.9
4.85-506.50.04118211.102199.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R8Q

4r8q


Resolution: 1.85→26.689 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.68
RfactorNum. reflection% reflection
Rfree0.2209 1489 5.06 %
Rwork0.1878 --
obs0.1894 29409 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.18 Å2 / Biso mean: 30.37 Å2 / Biso min: 8.72 Å2
Refinement stepCycle: final / Resolution: 1.85→26.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 13 294 3032
Biso mean--36.19 36.88 -
Num. residues----334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052807
X-RAY DIFFRACTIONf_angle_d0.9553795
X-RAY DIFFRACTIONf_chiral_restr0.066418
X-RAY DIFFRACTIONf_plane_restr0.004479
X-RAY DIFFRACTIONf_dihedral_angle_d15.4311050
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8501-1.90980.30651270.2712211283
1.9098-1.9780.27431280.2244240494
1.978-2.05720.26381240.20722558100
2.0572-2.15080.21411430.19362546100
2.1508-2.26410.23421320.18692578100
2.2641-2.40590.25181410.19092571100
2.4059-2.59150.23541350.20332592100
2.5915-2.8520.23751510.20092558100
2.852-3.26410.23391430.18972596100
3.2641-4.110.18691370.15962638100
4.11-26.6890.19111280.18082767100
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)
12.6982-0.83350.55822.5834-0.33532.0113-0.2348-0.64590.02350.54910.33680.5196-0.1117-0.33560.02790.22850.07560.08960.25570.00170.2591-3.242237.879438.0721
23.8516-1.1881-0.46973.35021.0321.34870.19480.384-0.689-0.5158-0.21021.16510.0645-0.19420.08030.18430.0295-0.05940.1902-0.02240.387-7.379625.527619.2921
33.3633-1.0060.51422.69330.56711.496-0.03280.04050.0052-0.05110.00170.1638-0.10170.01180.06130.10080.01770.00520.08820.0070.11742.646633.961126.6413
44.2703-2.7381-0.4363.31350.75440.4349-0.0590.1646-0.3568-0.13160.04740.02450.07970.08080.02920.1009-0.01220.03540.1443-0.0250.20513.455717.468419.9892
52.6837-1.3453-0.3132.92260.71651.3672-0.0885-0.0034-0.01410.11090.0472-0.1615-0.01940.0090.00720.0822-0.0087-0.01790.09990.01880.094218.980326.406829.7501
61.7903-0.9819-0.19222.55791.01433.8719-0.0457-0.012-0.0417-0.12710.1251-0.1763-0.26530.38410.0330.1408-0.01320.00060.1383-0.00930.164515.25130.408227.1396
73.5765-1.81140.06262.8217-1.02962.648-0.4781-0.4865-0.65450.89020.38360.65050.03080.06490.10960.42380.10660.05290.35060.07430.228912.815823.506548.0819
82.4637-0.8476-0.6973.90641.34263.9541-0.1778-0.231-0.4050.25450.01870.06340.01110.08040.12570.12740.0029-0.01880.14610.0410.162919.921620.001835.5799
93.039-0.35930.59862.8231-0.3824.987-0.1192-0.4377-0.82890.8089-0.1323-0.19730.52730.14270.04810.35660.0347-0.02720.28490.17360.402824.195611.594543.0172
102.6269-0.1202-0.4722.4762-0.21933.4054-0.2116-0.316-0.1150.47180.0282-0.5630.13430.34340.08410.19640.0121-0.08780.26380.08250.239129.420719.694238.8735
112.9852-0.2503-0.00862.64270.80383.4592-0.00770.2619-0.2335-0.20070.098-0.6469-0.09010.40680.05920.0975-0.02510.03410.1590.0340.276230.495122.578820.8442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1126 through 1155 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1156 through 1194 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1195 through 1245 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1246 through 1274 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1275 through 1309 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1310 through 1335 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1336 through 1363 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 1364 through 1380 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 1381 through 1397 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 1398 through 1428 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 1429 through 1459 )A0

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