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- PDB-4r8q: Structure and substrate recruitment of the human spindle checkpoi... -

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Basic information

Entry
Database: PDB / ID: 4r8q
TitleStructure and substrate recruitment of the human spindle checkpoint kinase bub1
ComponentsMitotic checkpoint serine/threonine-protein kinase BUB1
KeywordsTRANSFERASE / SPINDLE ASSEMBLY CHECKPOINT / MITOSIS / KINASE / ACTIVATION / KEN BOX / CDC20 / ATP-BINDING / CELL CYCLE / CELL DIVISION / DISEASE MUTATION / NUCLEOTIDE-BINDING / NUCLEUS / PHOSPHOPROTEIN / SERINE/THREONINE-PROTEIN KINASE
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 / intracellular membrane-bounded organelle / protein serine kinase activity / 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 / SAD / Resolution: 2.31 Å
AuthorsTomchick, D.R. / Yu, H.
CitationJournal: Mol.Cell / Year: 2008
Title: Structure and substrate recruitment of the human spindle checkpoint kinase Bub1.
Authors: Kang, J. / Yang, M. / Li, B. / Qi, W. / Zhang, C. / Shokat, K.M. / Tomchick, D.R. / Machius, M. / Yu, H.
History
DepositionSep 2, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionNov 12, 2014ID: 3E7E
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.pdbx_dist_value / _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_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_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

Downloads & links

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Assembly

Deposited unit
A: Mitotic checkpoint serine/threonine-protein kinase BUB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3234
Polymers41,8481
Non-polymers4763
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.768, 147.632, 47.196
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 41847.574 Da / Num. of mol.: 1 / Fragment: Kinase domain, unp residues 724-1085
Source method: isolated from a genetically manipulated source
Details: Cell line SF9 / Source: (gene. exp.) Homo sapiens (human) / Gene: BUB1, BUB1L / Plasmid: PBAC2 / 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.: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.29
Details: TO 15 MG/ML BUB1, ATP WAS ADDED TO A FINAL CONCENTRATION OF 10 MM. SITTING DROPS WERE MADE BY MIXING 1.5 MICROLITERS PROTEIN WITH 1.5 MICROLITERS CRYSTALLIZATION SOLUTION (20% W/V PEG 3350, ...Details: TO 15 MG/ML BUB1, ATP WAS ADDED TO A FINAL CONCENTRATION OF 10 MM. SITTING DROPS WERE MADE BY MIXING 1.5 MICROLITERS PROTEIN WITH 1.5 MICROLITERS CRYSTALLIZATION SOLUTION (20% W/V PEG 3350, 0.1 M SODIUM FORMATE PH 6.29, 25 MM DTT) AND EQUILIBRATING AGAINST 200 MICROLITERS OF RESERVOIR SOLUTION. LARGE SINGLE CRYSTALS WERE OBTAINED BY REPEATED SEEDING. THE CRYSTALS WERE CRYO-PROTECTED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 18% V/V GLYCEROL AND THEN FLASH-COOLED IN LIQUID PROPANE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, vapor diffusion, sitting drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2005 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. all: 16738 / Num. obs: 16738 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Biso Wilson estimate: 30.06 Å2 / Rmerge(I) obs: 0.037 / Χ2: 0.922 / Net I/σ(I): 14.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.32-2.365.60.7318620.791100
2.36-2.45.50.3538100.861100
2.4-2.455.60.3278360.871100
2.45-2.55.60.2738590.8731100
2.5-2.555.50.2168150.8161100
2.55-2.615.50.1898530.8261100
2.61-2.685.50.1638410.8791100
2.68-2.755.50.1348540.844199.9
2.75-2.835.50.1048420.831100
2.83-2.925.50.0878470.8541100
2.92-3.035.50.0698470.86199.9
3.03-3.155.50.0598680.9231100
3.15-3.295.50.0598421.2721100
3.29-3.475.50.0588491.658199.9
3.47-3.684.80.0635882.293167.6
3.68-3.974.90.0468341.838197.4
3.97-4.375.20.0278610.82199.9
4.37-550.0168710.393199.8
5-6.295.50.0148830.319199.9
6.29-504.90.0118760.245191.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.31→32.506 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 27.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2641 1288 7.74 %random
Rwork0.2224 ---
obs0.2256 16638 97.14 %-
all-16638 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.2 Å2 / Biso mean: 48.1761 Å2 / Biso min: 9.2 Å2
Refine analyzeLuzzati coordinate error free: 0.314 Å
Refinement stepCycle: LAST / Resolution: 2.31→32.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2693 0 29 16 2738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052805
X-RAY DIFFRACTIONf_angle_d0.8223774
X-RAY DIFFRACTIONf_chiral_restr0.03405
X-RAY DIFFRACTIONf_plane_restr0.003470
X-RAY DIFFRACTIONf_dihedral_angle_d13.3941038
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3103-2.40280.37621510.32271626177795
2.4028-2.51210.33871400.277817201860100
2.5121-2.64450.32831390.258117481887100
2.6445-2.81010.29311460.252217141860100
2.8101-3.02690.27831490.250717501899100
3.0269-3.33120.27811490.244717351884100
3.3312-3.81260.27781230.23591484160784
3.8126-4.8010.21181480.16461760190899
4.801-32.50910.21131430.18671813195696
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)
10.2127-0.0120.34760.18-0.14650.9896-0.0540.18640.6417-0.1355-0.05940.1436-0.02510.4207-0.16180.1472-0.0258-0.09560.1961-0.06870.5283-9.789327.8955-11.6253
20.33330.0168-0.1260.0218-0.0140.0237-0.16530.9438-0.1394-0.52390.2180.07760.0890.31070.10380.3596-0.0259-0.08451.00140.0433-0.4053-16.854316.7489-31.8366
30.47620.1310.32650.35990.23390.4246-0.06180.2296-0.26330.11880.3115-0.58930.1740.53330.15320.20940.0384-0.09350.21170.0140.2234-16.010416.05-17.3741
40.6285-0.1255-0.45390.23830.16490.2919-0.0499-0.04-0.06870.03460.0172-0.02050.08160.0573-0.15370.233-0.0089-0.07580.15190.02290.1656-33.004614.7615-12.9896
50.36550.1692-0.2440.2610.04650.2917-0.0236-0.1450.89790.04310.13890.12560.02580.11540.33760.13590.007-0.07080.1526-0.09140.3583-36.850828.1196-4.5012
60.9409-0.2863-0.55780.10160.14440.3869-0.4565-1.0247-0.14760.11740.40040.26730.18410.28230.07210.41510.0797-0.09430.37980.09730.2893-38.850314.76562.4269
70.2087-0.00780.02810.03520.02680.0914-0.08060.2584-0.22430.28750.17590.23230.23020.29140.02110.58230.07850.03240.2172-0.3530.713-41.14814.5665-21.8397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 736 through 766 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 767 through 804 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 805 through 866 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 867 through 952 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 953 through 1036 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1037 through 1065 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1066 through 1083 )A0

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