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- PDB-4qpm: Structure of Bub1 kinase domain -

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Basic information

Entry
Database: PDB / ID: 4qpm
TitleStructure of Bub1 kinase domain
ComponentsMitotic checkpoint serine/threonine-protein kinase BUB1
KeywordsTRANSFERASE
Function / homology
Function and homology information


histone H2A kinase activity / positive regulation of maintenance of mitotic sister chromatid cohesion, centromeric / regulation of sister chromatid cohesion / regulation of chromosome segregation / meiotic sister chromatid cohesion, centromeric / outer kinetochore / mitotic spindle assembly checkpoint signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation ...histone H2A kinase activity / positive regulation of maintenance of mitotic sister chromatid cohesion, centromeric / regulation of sister chromatid cohesion / regulation of chromosome segregation / meiotic sister chromatid cohesion, centromeric / outer kinetochore / mitotic spindle assembly checkpoint signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / chromosome segregation / RHO GTPases Activate Formins / kinetochore / Separation of Sister Chromatids / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / cell division / protein serine kinase activity / protein serine/threonine kinase activity / intracellular membrane-bounded organelle / apoptotic process / nucleoplasm / ATP binding / nucleus / membrane / cytosol
Similarity search - Function
GTP Cyclohydrolase I; Chain A, domain 1 - #20 / GTP Cyclohydrolase I; Chain A, domain 1 / 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 / Helix non-globular / Special / Transferase(Phosphotransferase) domain 1 ...GTP Cyclohydrolase I; Chain A, domain 1 - #20 / GTP Cyclohydrolase I; Chain A, domain 1 / 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 / Helix non-globular / Special / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Mitotic checkpoint serine/threonine-protein kinase BUB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å
AuthorsLin, Z.H. / Jia, L.Y. / Tomchick, D.R. / Luo, X.L. / Yu, H.T.
CitationJournal: Structure / Year: 2014
Title: Substrate-Specific Activation of the Mitotic Kinase Bub1 through Intramolecular Autophosphorylation and Kinetochore Targeting.
Authors: Lin, Z. / Jia, L. / Tomchick, D.R. / Luo, X. / Yu, H.
History
DepositionJun 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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: Mitotic checkpoint serine/threonine-protein kinase BUB1
B: Mitotic checkpoint serine/threonine-protein kinase BUB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,31311
Polymers82,2552
Non-polymers1,0589
Water4,107228
1
A: Mitotic checkpoint serine/threonine-protein kinase BUB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6395
Polymers41,1281
Non-polymers5114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mitotic checkpoint serine/threonine-protein kinase BUB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6746
Polymers41,1281
Non-polymers5475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.013, 47.180, 93.146
Angle α, β, γ (deg.)90.00, 107.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mitotic checkpoint serine/threonine-protein kinase BUB1 / hBUB1 / BUB1A


Mass: 41127.668 Da / Num. of mol.: 2 / Fragment: UNP residues 749-1094
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BUB1, BUB1L / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O43683, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / 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.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 293 K / pH: 7
Details: 20% PEG3350, 1% Tryptone, 10 mM DTT, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 37658

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.202→36.882 Å / SU ML: 0.32 / σ(F): 1.37 / Phase error: 29.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2685 1884 5.01 %
Rwork0.2293 --
obs0.2313 37581 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.202→36.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5356 0 61 228 5645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055600
X-RAY DIFFRACTIONf_angle_d0.7477542
X-RAY DIFFRACTIONf_dihedral_angle_d12.3332083
X-RAY DIFFRACTIONf_chiral_restr0.028807
X-RAY DIFFRACTIONf_plane_restr0.003939
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2024-2.26190.32541300.26412430X-RAY DIFFRACTION87
2.2619-2.32850.29411340.25612567X-RAY DIFFRACTION93
2.3285-2.40360.34071630.24692673X-RAY DIFFRACTION97
2.4036-2.48950.33261310.25712777X-RAY DIFFRACTION99
2.4895-2.58920.29721370.25342782X-RAY DIFFRACTION100
2.5892-2.7070.30431490.25082753X-RAY DIFFRACTION100
2.707-2.84960.27161350.25462788X-RAY DIFFRACTION100
2.8496-3.02810.2741510.25272786X-RAY DIFFRACTION100
3.0281-3.26180.30571510.242798X-RAY DIFFRACTION100
3.2618-3.58980.27241420.22772825X-RAY DIFFRACTION100
3.5898-4.10860.25341550.2052783X-RAY DIFFRACTION100
4.1086-5.17420.22331690.19642820X-RAY DIFFRACTION100
5.1742-36.88670.2391370.22662915X-RAY DIFFRACTION100
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)
10.7577-0.3139-0.81710.27670.54470.9722-0.1477-0.54780.01890.24170.00050.0204-0.1562-0.0115-0.0230.3702-0.0265-0.06580.27550.02610.30094.82185.556151.9812
20.0410.1220.01020.40240.10411.6455-0.18430.15370.5218-0.0494-0.0162-0.0879-1.05120.1794-0.35180.4734-0.1583-0.06930.28260.13110.432910.231917.645337.7528
30.61470.21110.28830.24620.36320.9205-0.08430.06760.0178-0.0716-0.0635-0.04510.06330.218200.22830.0306-0.01010.24620.04250.22944.13971.423832.9826
40.3890.00260.33770.13190.00960.23410.15150.0918-0.0320.0916-0.03980.1217-0.275-0.145800.27280.02170.03830.25840.05060.2887-3.7488-4.983640.8907
50.4196-0.16860.06490.0731-0.05180.12940.0416-0.0504-0.25760.0229-0.0787-0.0212-0.1098-0.129300.2886-0.01790.02530.30560.05020.3257-11.0506-7.902133.8999
60.1318-0.10380.06790.2418-0.2630.20730.08380.01670.00730.1650.0346-0.1617-0.0347-0.32330.00010.3679-0.0669-0.06610.4596-0.02330.3183-18.0386-7.416822.5911
70.9549-0.06940.19440.73530.53781.86960.04180.1004-0.3922-0.0529-0.0156-0.2040.5323-0.18570.17380.32990.02520.0170.2139-0.02350.3449-4.8118-15.196622.328
80.8587-0.43280.36350.79070.06140.2950.14280.2781-0.1191-0.1788-0.2953-0.1454-0.12680.1908-0.01060.3837-0.09810.07450.40640.07930.30024.91528.257214.2957
90.2259-0.16580.12680.3354-0.0280.10880.0835-0.05670.20080.14970.2228-0.4599-0.0773-0.03870.0170.2781-0.0709-0.00010.3367-0.03530.331847.52621.172719.8801
102.0099-0.71580.15260.4068-0.59042.12410.42470.2005-0.95420.02330.005-0.07951.3417-0.51380.59210.6619-0.1523-0.16560.05920.03750.461334.82431.782919.9008
110.8101-0.05630.54560.3704-0.04411.09190.1416-0.3760.11920.2012-0.0910.04690.0699-0.3080.00030.2732-0.04930.00230.2853-0.03070.213728.041518.1813.9953
120.23270.12260.13380.4549-0.27740.38720.2251-0.218-0.12490.1594-0.0988-0.1233-0.0077-0.21990.00640.2288-0.0907-0.01960.2905-0.0340.221628.82422.187211.8552
130.15770.29650.5542.18061.77032.1259-0.15520.2854-0.462-0.6810.03860.5141-0.5143-0.2751-0.08940.3115-0.1810.04820.6001-0.03120.488242.893429.35760.3041
140.45650.2184-0.19790.2736-0.14490.53010.06740.28090.03470.0538-0.0966-0.0315-0.0760.214200.2416-0.0087-0.00410.32340.02850.245827.021127.2153-6.6332
150.72340.1479-0.39060.1834-0.00560.5162-0.23850.55860.6911-0.1390.04520.0566-0.5980.0455-0.01740.3901-0.0096-0.06670.28690.03890.432627.790136.7507-2.0262
160.8158-0.05810.37310.326-0.21611.7621-0.2481-0.4064-0.0470.09450.1384-0.1313-0.3494-0.3763-0.32370.21920.00680.1160.33510.03070.375711.503524.7565.3269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 739:777 )A739 - 777
2X-RAY DIFFRACTION2( CHAIN A AND RESID 778:817 )A778 - 817
3X-RAY DIFFRACTION3( CHAIN A AND RESID 818:930 )A818 - 930
4X-RAY DIFFRACTION4( CHAIN A AND RESID 931:971 )A931 - 971
5X-RAY DIFFRACTION5( CHAIN A AND RESID 972:1000 )A972 - 1000
6X-RAY DIFFRACTION6( CHAIN A AND RESID 1001:1024 )A1001 - 1024
7X-RAY DIFFRACTION7( CHAIN A AND RESID 1025:1065 )A1025 - 1065
8X-RAY DIFFRACTION8( CHAIN A AND RESID 1066:1083 )A1066 - 1083
9X-RAY DIFFRACTION9( CHAIN B AND RESID 739:766 )B739 - 766
10X-RAY DIFFRACTION10( CHAIN B AND RESID 767:804 )B767 - 804
11X-RAY DIFFRACTION11( CHAIN B AND RESID 805:910 )B805 - 910
12X-RAY DIFFRACTION12( CHAIN B AND RESID 911:955 )B911 - 955
13X-RAY DIFFRACTION13( CHAIN B AND RESID 956:983 )B956 - 983
14X-RAY DIFFRACTION14( CHAIN B AND RESID 984:1024 )B984 - 1024
15X-RAY DIFFRACTION15( CHAIN B AND RESID 1025:1046 )B1025 - 1046
16X-RAY DIFFRACTION16( CHAIN B AND RESID 1047:1081 )B1047 - 1081

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