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- PDB-2i3s: Bub3 complex with Bub1 GLEBS motif -

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Basic information

Entry
Database: PDB / ID: 2i3s
TitleBub3 complex with Bub1 GLEBS motif
Components
  • Cell cycle arrest protein
  • Checkpoint serine/threonine-protein kinase
KeywordsCELL CYCLE / WD40 protein / beta-propeller / GLEBS motif / mitotic spindle checkpoint
Function / homology
Function and homology information


bub1-bub3 complex / Inactivation of APC/C via direct inhibition of the APC/C complex / mitotic DNA integrity checkpoint signaling / : / mitotic checkpoint complex / sister chromatid biorientation / meiotic sister chromatid cohesion, centromeric / outer kinetochore / condensed chromosome, centromeric region / protein localization to kinetochore ...bub1-bub3 complex / Inactivation of APC/C via direct inhibition of the APC/C complex / mitotic DNA integrity checkpoint signaling / : / mitotic checkpoint complex / sister chromatid biorientation / meiotic sister chromatid cohesion, centromeric / outer kinetochore / condensed chromosome, centromeric region / protein localization to kinetochore / positive regulation of protein autoubiquitination / mitotic spindle assembly checkpoint signaling / ubiquitin binding / macroautophagy / kinetochore / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / identical protein binding / nucleus
Similarity search - Function
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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H ...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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Protein kinase domain / WD40-repeat-containing domain superfamily / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Spindle assembly checkpoint protein BUB3 / Spindle assembly checkpoint serine/threonine-protein kinase BUB1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLarsen, N.A. / Harrison, S.C.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural analysis of Bub3 interactions in the mitotic spindle checkpoint.
Authors: Larsen, N.A. / Al-Bassam, J. / Wei, R.R. / Harrison, S.C.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of the spindle assembly checkpoint protein Bub3.
Authors: Larsen, N.A. / Harrison, S.C.
History
DepositionAug 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 2, 2014Group: Source and taxonomy
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell cycle arrest protein
B: Checkpoint serine/threonine-protein kinase
C: Cell cycle arrest protein
D: Checkpoint serine/threonine-protein kinase
E: Cell cycle arrest protein
F: Checkpoint serine/threonine-protein kinase


Theoretical massNumber of molelcules
Total (without water)131,7146
Polymers131,7146
Non-polymers00
Water11,602644
1
A: Cell cycle arrest protein
B: Checkpoint serine/threonine-protein kinase


Theoretical massNumber of molelcules
Total (without water)43,9052
Polymers43,9052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-16 kcal/mol
Surface area16090 Å2
MethodPISA
2
C: Cell cycle arrest protein
D: Checkpoint serine/threonine-protein kinase


Theoretical massNumber of molelcules
Total (without water)43,9052
Polymers43,9052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-16 kcal/mol
Surface area15550 Å2
MethodPISA
3
E: Cell cycle arrest protein
F: Checkpoint serine/threonine-protein kinase


Theoretical massNumber of molelcules
Total (without water)43,9052
Polymers43,9052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-15 kcal/mol
Surface area15750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.656, 79.181, 142.582
Angle α, β, γ (deg.)90.00, 98.34, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly consists of a single heterodimer of Bub3 and Bub1 GLEBS peptide. There are 3 heterodimers in the asymmetric unit.

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Components

#1: Protein Cell cycle arrest protein


Mass: 39554.633 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BUB3, YOR026W, OR26.16 / Production host: Escherichia coli (E. coli) / References: UniProt: P26449
#2: Protein/peptide Checkpoint serine/threonine-protein kinase / Bub1 GLEBS motif


Mass: 4349.952 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Chemically synthesized peptide. / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P41695, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 18% PEG 3K 200 mM NaCl 100 mM Cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9778 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 79711 / % possible obs: 90.6 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2.3 / Rsym value: 0.054
Reflection shellResolution: 1.9→1.97 Å / % possible all: 68.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1U4C

1u4c


Resolution: 1.9→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.262 3811 Random
Rwork0.219 --
all0.221 75071 -
obs0.221 75071 -
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8798 0 0 644 9442
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0055
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d0.72

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