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- PDB-5dmz: Structure of human Bub1 kinase domain phosphorylated at Ser969 -

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Basic information

Entry
Database: PDB / ID: 5dmz
TitleStructure of human Bub1 kinase domain phosphorylated at Ser969
ComponentsMitotic checkpoint serine/threonine-protein kinase BUB1
KeywordsTRANSFERASE / kinase / phosphorylation
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 / non-specific serine/threonine protein kinase / protein kinase activity / cell division / phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / apoptotic process / nucleoplasm / ATP binding / membrane / nucleus / 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: 2.4 Å
AuthorsBreit, C. / Weir, J.R. / Musacchio, A.
Funding support2items
OrganizationGrant numberCountry
European Research Council (ERC) Advanced Investigator award RECEPIANCE
German Research Foundation1093
CitationJournal: Plos One / Year: 2015
Title: Role of Intrinsic and Extrinsic Factors in the Regulation of the Mitotic Checkpoint Kinase Bub1.
Authors: Breit, C. / Bange, T. / Petrovic, A. / Weir, J.R. / Muller, F. / Vogt, D. / Musacchio, A.
History
DepositionSep 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Oct 19, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)84,7526
Polymers83,8492
Non-polymers9034
Water43224
1
A: Mitotic checkpoint serine/threonine-protein kinase BUB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3763
Polymers41,9251
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitotic checkpoint serine/threonine-protein kinase BUB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3763
Polymers41,9251
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.380, 66.340, 106.540
Angle α, β, γ (deg.)90.00, 98.34, 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: 41924.547 Da / Num. of mol.: 2 / Fragment: UNP residues 726-1085
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BUB1, BUB1L / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: O43683, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 0.2 M NaCl, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→56.1 Å / Num. all: 33923 / Num. obs: 33866 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.99
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 6.9 % / Rmerge(I) obs: 2.4 / Mean I/σ(I) obs: 1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERv6.2.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E7E

3e7e
PDB Unreleased entry


Resolution: 2.4→43.304 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2451 1692 5 %
Rwork0.2105 --
obs0.2122 33831 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→43.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5526 0 56 24 5606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045728
X-RAY DIFFRACTIONf_angle_d0.8537748
X-RAY DIFFRACTIONf_dihedral_angle_d14.3732134
X-RAY DIFFRACTIONf_chiral_restr0.03828
X-RAY DIFFRACTIONf_plane_restr0.004972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47060.40571390.38562639X-RAY DIFFRACTION100
2.4706-2.55040.38691400.37722647X-RAY DIFFRACTION100
2.5504-2.64150.40571380.35172633X-RAY DIFFRACTION100
2.6415-2.74730.34051410.32942689X-RAY DIFFRACTION100
2.7473-2.87230.34561410.28322670X-RAY DIFFRACTION100
2.8723-3.02370.36471410.26732668X-RAY DIFFRACTION100
3.0237-3.21310.27241400.25412672X-RAY DIFFRACTION100
3.2131-3.4610.28351410.242673X-RAY DIFFRACTION100
3.461-3.80910.21351420.20482689X-RAY DIFFRACTION100
3.8091-4.35990.20641410.1752677X-RAY DIFFRACTION100
4.3599-5.49130.17491430.15222715X-RAY DIFFRACTION100
5.4913-43.31070.21071450.1682767X-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)
12.5343-0.3281-0.27730.9759-0.47672.80330.06410.06570.07580.0187-0.1075-0.7621-0.21090.91730.11250.61930.00110.07270.9369-0.14351.04612.07683.6234-50.9779
22.7842-1.18772.70623.7719-0.12853.02160.06640.1599-1.85950.3015-0.5891-1.67630.49462.72560.29891.28840.2467-0.52791.06570.13951.0878-8.1601-8.7772-27.4563
34.9523-1.7961-0.8974.9221.19972.0954-0.1396-0.5897-0.90031.11250.0576-0.08790.84880.8431-0.05970.9106-0.0022-0.10860.78950.07440.7594-7.6172-2.0842-32.3131
42.22491.12722.63733.2384.64357.2376-0.2245-0.37221.56271.11670.5286-0.32360.35-0.1832-0.13880.7696-0.0212-0.07740.8946-0.05650.8509-9.71476.4125-27.6112
51.96891.5765-1.09042.4957-1.13165.5899-0.009-0.1392-0.0330.05840.0084-0.8334-0.12730.75220.00690.5424-0.0101-0.02210.7801-0.07790.8713-5.7418.2003-42.3131
65.0987-0.1775-0.31644.4008-0.30874.00750.0495-0.21530.01730.08590.0543-0.1391-0.1646-0.0128-0.07840.4993-0.03880.01810.4531-0.03410.445-24.921110.5338-44.8696
73.23690.9234-0.19722.0096-6.75354.1760.8076-1.31491.26670.72330.70030.1016-1.4699-0.6062-1.56641.456-0.29270.31871.19010.01410.8837-25.464620.5233-32.6766
83.9364-3.0958-0.575.85624.49294.8446-1.6128-2.68690.42730.94731.2641.9044-0.9155-0.83590.33091.48240.12190.25071.2529-0.13011.0691-26.258524.6578-40.6774
94.23850.5382-0.41533.2796-0.17436.5790.0308-0.04820.0128-0.32790.0687-0.636-0.67230.7288-0.11190.54630.00060.13850.6980.05630.8062-9.723611.9968-54.2041
107.71292.96351.86618.7974-2.31252.0829-0.02830.1126-0.2861-0.16510.52560.3009-0.2633-0.1164-0.65910.60840.00950.12360.6962-0.03020.7313-15.09670.6535-60.7655
117.13681.6467-1.4124.5919-0.49913.83010.10770.8771-0.0471-0.42640.01230.27480.1476-0.3363-0.07580.6766-0.03060.00620.6175-0.01890.5293-26.25966.6556-60.4142
124.4551-3.81781.98413.3132-1.45992.08240.94460.3352-0.64130.6577-0.48722.09180.4489-0.8611-0.81310.8447-0.0968-0.02021.28070.00221.0995-44.97477.3949-56.5137
132.0764-1.8131-1.71977.63252.85778.63330.19660.40910.1502-0.9071-0.1872-0.0666-0.0951-0.1431-0.0820.4240.0255-0.01990.46770.08170.4451-31.041119.0328-56.4234
148.4192-5.77963.48459.7346-7.00168.4489-0.5798-0.2344-0.44021.28270.76660.7229-0.4795-0.618-0.29650.7203-0.01050.08680.67230.02840.5274-33.669812.0586-33.3263
153.6672-2.5736-3.03692.66091.5332.9524-0.1073-0.1690.09171.19050.1589-0.0080.772-1.12740.03491.37170.17680.26530.83590.02060.6951-26.28960.704-27.1085
162.7274-0.0537-2.14710.4532-0.07663.17330.0725-0.40990.02840.461-0.0294-0.6984-0.32560.97590.06780.9183-0.0271-0.20821.1607-0.00730.9557-6.452917.35337.52
177.72631.7375-5.39082.37170.93076.075-0.9929-1.85921.8904-0.38290.40130.8861-0.52310.84280.42611.0412-0.12290.0440.9088-0.09151.0859-5.249732.1454-9.9146
185.65270.62630.4632.4643-0.69214.87650.26330.58320.7347-0.2558-0.0171-0.5917-0.86710.3826-0.23820.8708-0.05930.16620.62690.00270.9014-9.809926.3215-15.0561
196.3447-3.0715-1.74923.30314.10036.40990.00020.8130.1471-0.6397-0.0888-0.73180.47340.4684-0.22010.87740.04310.12940.80190.05030.8394-10.338222.1217-18.3081
203.1729-0.3482-1.90711.635-0.9124.88520.08830.0331-0.27630.3540.3154-0.52590.64010.4949-0.24650.72720.1064-0.1010.7239-0.0450.7795-11.423913.1887-5.0544
213.41891.3590.02922.70260.69073.22240.01440.117-0.10580.32520.1078-0.08010.0908-0.0212-0.0350.6420.08570.0370.5003-0.02150.5277-27.409513.7233-7.5467
229.23065.1898-0.23133.1212-1.35337.97790.57360.4552-1.20870.76520.3471-1.2830.95170.0056-1.03091.34250.19280.0190.8296-0.01290.8601-26.44324.9795-19.1744
231.2111.9354-0.02235.86912.39025.0661-0.25282.10290.5812-0.76642.2459-0.16160.65511.8022-1.86141.3629-0.1848-0.06931.1923-0.26921.3365-30.4398-1.8495-12.3155
246.7982-2.48952.41683.8299-3.04232.4760.1236-0.0875-0.31860.33460.2492-0.1335-0.4238-0.0916-0.54330.6255-0.0593-0.06720.49590.00970.579-18.302410.65134.6871
254.08890.61681.10263.04250.75353.66070.1664-0.5270.27290.5806-0.17680.2483-0.0848-0.06710.0310.99370.02450.09690.56730.01030.5084-33.721417.25577.5728
260.94032.42451.96976.26835.08124.13950.3915-0.10221.4818-0.0003-0.7481.1724-1.8804-0.80480.46591.78040.14550.13170.8755-0.08681.0253-52.342316.2337-1.8623
272.2344-0.05520.0764.77091.51156.41760.1832-0.3127-0.02570.917-0.27820.10170.1791-0.1880.0930.7458-0.05880.09550.47780.10840.5651-39.76933.66590.5304
289.57626.1429-1.14013.7797-0.55484.2616-0.6110.12270.1225-0.77730.5988-0.03410.4227-0.35940.07110.86130.05840.01750.59260.03870.5027-32.988813.9114-22.3703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 735:774)
2X-RAY DIFFRACTION2(chain A and resid 775:779)
3X-RAY DIFFRACTION3(chain A and resid 780:806)
4X-RAY DIFFRACTION4(chain A and resid 816:818)
5X-RAY DIFFRACTION5(chain A and resid 819:870)
6X-RAY DIFFRACTION6(chain A and resid 871:929)
7X-RAY DIFFRACTION7(chain A and resid 930:934)
8X-RAY DIFFRACTION8(chain A and resid 935:938)
9X-RAY DIFFRACTION9(chain A and resid 939:961)
10X-RAY DIFFRACTION10(chain A and resid 962:972)
11X-RAY DIFFRACTION11(chain A and resid 973:1017)
12X-RAY DIFFRACTION12(chain A and resid 1018:1021)
13X-RAY DIFFRACTION13(chain A and resid 1022:1063)
14X-RAY DIFFRACTION14(chain A and resid 1064:1080)
15X-RAY DIFFRACTION15(chain A and resid 1081:1083)
16X-RAY DIFFRACTION16(chain B and resid 735:769)
17X-RAY DIFFRACTION17(chain B and resid 770:775)
18X-RAY DIFFRACTION18(chain B and resid 776:801)
19X-RAY DIFFRACTION19(chain B and resid 802:806)
20X-RAY DIFFRACTION20(chain B and resid 816:858)
21X-RAY DIFFRACTION21(chain B and resid 859:925)
22X-RAY DIFFRACTION22(chain B and resid 926:934)
23X-RAY DIFFRACTION23(chain B and resid 935:938)
24X-RAY DIFFRACTION24(chain B and resid 939:960)
25X-RAY DIFFRACTION25(chain B and resid 961:1017)
26X-RAY DIFFRACTION26(chain B and resid 1018:1021)
27X-RAY DIFFRACTION27(chain B and resid 1022:1065)
28X-RAY DIFFRACTION28(chain B and resid 1066:1083)

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