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- PDB-3esl: Crystal structure of the conserved N-terminal domain of the mitot... -

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Basic information

Entry
Database: PDB / ID: 3esl
TitleCrystal structure of the conserved N-terminal domain of the mitotic checkpoint component BUB1
ComponentsCheckpoint serine/threonine-protein kinase BUB1
KeywordsCELL CYCLE / BUB1 / MITOTIC SPINDLE CHECKPOINT / TPR MOTIF / ALL-ALPHA DOMAIN / MAD3-LIKE DOMAIN / CHROMOSOME INSTABILITY / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / NUCLEUS / PHOSPHORYLATION / SERINE/THREONINE-PROTEIN KINASE / TRANSFERASE / KINETOCHORE LOCALIZATION / Phosphoprotein
Function / homology
Function and homology information


bub1-bub3 complex / Inactivation of APC/C via direct inhibition of the APC/C complex / centromere complex assembly / sister chromatid biorientation / meiotic sister chromatid cohesion, centromeric / outer kinetochore / condensed chromosome, centromeric region / protein localization to kinetochore / mitotic spindle assembly checkpoint signaling / macroautophagy ...bub1-bub3 complex / Inactivation of APC/C via direct inhibition of the APC/C complex / centromere complex assembly / sister chromatid biorientation / meiotic sister chromatid cohesion, centromeric / outer kinetochore / condensed chromosome, centromeric region / protein localization to kinetochore / mitotic spindle assembly checkpoint signaling / macroautophagy / kinetochore / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex / ATP binding / identical protein binding / nucleus
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2070 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #930 / Mad3/Bub1 homology region 2 / Mad3/BUB1 homology region 2 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2070 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #930 / Mad3/Bub1 homology region 2 / Mad3/BUB1 homology region 2 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Budding uninhibited by benzimidazole-related protein / Checkpoint serine/threonine-protein kinase BUB1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.74 Å
AuthorsBolanos-Garcia, V.M. / Chirgadze, D.Y. / Blundell, T.L.
CitationJournal: Structure / Year: 2009
Title: The Crystal Structure of the N-Terminal Region of BUB1 Provides Insight into the Mechanism of BUB1 Recruitment to Kinetochores.
Authors: Bolanos-Garcia, V.M. / Kiyomitsu, T. / D'Arcy, S. / Chirgadze, D.Y. / Grossmann, J.G. / Matak-Vinkovic, D. / Venkitaraman, A.R. / Yanagida, M. / Robinson, C.V. / Blundell, T.L.
History
DepositionOct 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Checkpoint serine/threonine-protein kinase BUB1
B: Checkpoint serine/threonine-protein kinase BUB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1784
Polymers48,7632
Non-polymers4152
Water4,270237
1
A: Checkpoint serine/threonine-protein kinase BUB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5892
Polymers24,3821
Non-polymers2071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Checkpoint serine/threonine-protein kinase BUB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5892
Polymers24,3821
Non-polymers2071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.304, 59.784, 71.299
Angle α, β, γ (deg.)90.00, 97.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Checkpoint serine/threonine-protein kinase BUB1


Mass: 24381.609 Da / Num. of mol.: 2 / Fragment: CONSERVED N-TERMINAL DOMAIN (RESIDUES 29-230)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: YJM789 / Gene: BUB1, G7542, YGR188C / Production host: Escherichia coli (E. coli) / References: UniProt: P41695, UniProt: A6ZUJ9*PLUS
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.82 Å3/Da / Density % sol: 56.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 9.6
Details: LITHIUM SALT, pH 9.60, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.977
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.74→34.92 Å / Num. obs: 54924 / % possible obs: 98.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 16.8
Reflection shellResolution: 1.74→1.78 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.249 / Rsym value: 0.249 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIXmodel building
REFMAC5.2.0019refinement
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.74→34.92 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.757 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2783 5.1 %RANDOM
Rwork0.19 ---
obs0.19 54921 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.41 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.74→34.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3464 0 26 237 3727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223572
X-RAY DIFFRACTIONr_angle_refined_deg1.0751.9684827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7585414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62523.96202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0215664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5071532
X-RAY DIFFRACTIONr_chiral_restr0.0730.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022750
X-RAY DIFFRACTIONr_nbd_refined0.1960.21677
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22533
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2198
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4350.221
X-RAY DIFFRACTIONr_mcbond_it2.30952136
X-RAY DIFFRACTIONr_mcangle_it3.15863329
X-RAY DIFFRACTIONr_scbond_it3.08351662
X-RAY DIFFRACTIONr_scangle_it4.7057.51498
LS refinement shellResolution: 1.74→1.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 188 -
Rwork0.241 3621 -
obs--92.18 %

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