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

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Basic information

Entry
Database: PDB / ID: 6jkm
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 / heterochromatin formation / kinetochore / protein kinase activity / protein phosphorylation / ATP 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
ADENOSINE-5'-DIPHOSPHATE / Bub1-related kinase / Mitotic checkpoint control protein kinase BUB1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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)40,1725
Polymers39,6041
Non-polymers5684
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-26 kcal/mol
Surface area16010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.333, 61.979, 96.232
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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging 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: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Feb 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 26399 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.104 / Χ2: 0.899 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.95-1.984.70.57613070.758199.5
1.98-2.0250.59212530.81100
2.02-2.065.10.47913300.783199.8
2.06-2.15.20.4512720.9871100
2.1-2.155.30.34613160.8251100
2.15-2.25.30.29613120.8071100
2.2-2.255.40.3212831.0941100
2.25-2.315.40.27313160.8771100
2.31-2.385.50.21913250.8371100
2.38-2.465.50.20712860.8061100
2.46-2.545.50.19112950.8691100
2.54-2.655.50.16713090.8421100
2.65-2.775.50.14213270.9011100
2.77-2.915.50.12213150.9081100
2.91-3.15.50.10113330.8921100
3.1-3.335.40.07913270.943199.9
3.33-3.675.30.07313391.1511100
3.67-4.25.10.06313441.166199.9
4.2-5.2950.05113650.944199.7
5.29-504.80.04814450.775198.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R8Q

4r8q


Resolution: 1.95→37.372 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.78
RfactorNum. reflection% reflection
Rfree0.2264 1145 5.11 %
Rwork0.1782 --
obs0.1807 22393 84.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.93 Å2 / Biso mean: 26.54 Å2 / Biso min: 9.11 Å2
Refinement stepCycle: final / Resolution: 1.95→37.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 35 255 3015
Biso mean--17.84 35.49 -
Num. residues----334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082830
X-RAY DIFFRACTIONf_angle_d1.0953835
X-RAY DIFFRACTIONf_chiral_restr0.045422
X-RAY DIFFRACTIONf_plane_restr0.005480
X-RAY DIFFRACTIONf_dihedral_angle_d15.2231057
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-2.03820.2719690.2021159951
2.0382-2.14560.2728840.1868189060
2.1456-2.280.22431410.1937220872
2.28-2.4560.2551520.202282390
2.456-2.70310.25551560.2007312599
2.7031-3.09410.23271700.19643141100
3.0941-3.89760.21481880.16673177100
3.8976-37.3720.20851850.1565328599
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)
10.72560.64370.5760.6610.60650.5658-0.2876-0.0953-0.02330.13420.05790.358-0.1101-0.0485-0.5070.16120.10660.12810.16590.02830.1105-3.234837.670938.6219
20.0619-0.0202-0.07390.05310.04840.13030.07080.18850.0567-0.1358-0.13690.2719-0.024-0.27320.00790.18170.0227-0.04210.1703-0.04540.3902-11.714328.197119.7739
30.4622-0.06060.04260.07760.02650.01980.08570.1774-0.3020.0224-0.07640.217-0.1614-0.07590.00150.23250.039-0.00410.1317-0.00820.1941-3.41925.24117.5152
40.0846-0.1315-0.04310.16890.08160.1133-0.0018-0.0243-0.03040.0583-0.01550.028-0.0773-0.02060.00060.13410.0061-0.00240.1076-0.00040.164.056734.264328.3905
50.09960.04210.07170.07320.08160.0953-0.08810.0984-0.03310.05430.01510.02310.02520.0077-0.0510.1399-0.01010.03210.1339-0.01110.201110.597718.832821.7618
60.3146-0.10570.09280.2992-0.06460.3793-0.11640.0064-0.0140.06850.0523-0.0677-0.06970.0698-0.0620.1013-0.0064-0.00990.09810.01060.103517.446328.133229.3452
70.6741-0.095-0.06310.14260.0870.0635-0.1651-0.2729-0.28880.35140.12020.0706-0.09470.09450.01610.25850.08660.03530.24410.1060.103113.002923.740648.8121
80.02630.00350.02020.0218-0.02890.0665-0.0629-0.0682-0.08750.1639-0.0145-0.02030.03090.01450.00480.1895-0.0062-0.03530.1880.02690.164320.072320.146736.3714
90.1121-0.0262-0.03820.0708-0.02530.0289-0.09820.0359-0.23340.18480.01430.09790.20360.0403-0.05190.31670.0765-0.00130.23820.19940.253624.658912.066644.0307
100.60340.3016-0.2130.3403-0.06860.2788-0.0906-0.2206-0.14860.1865-0.0919-0.2087-0.03220.1596-0.21260.18060.0194-0.03970.22970.05340.137529.593419.931939.6355
110.1056-0.13460.1050.1926-0.17280.209-0.0740.1098-0.0888-0.0361-0.0234-0.1677-0.14610.1618-0.17430.1184-0.03620.02530.22560.00280.166330.488122.695821.3252
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 1172 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1173 through 1199 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1200 through 1241 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1242 through 1274 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1275 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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