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- PDB-2i3t: Bub3 complex with Mad3 (BubR1) GLEBS motif -

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Basic information

Entry
Database: PDB / ID: 2i3t
TitleBub3 complex with Mad3 (BubR1) GLEBS motif
Components
  • Cell cycle arrest protein
  • Spindle assembly checkpoint component
KeywordsCELL CYCLE / WD40 protein / beta propeller / 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 / distributive segregation / mitotic checkpoint complex / meiotic sister chromatid cohesion, centromeric / positive regulation of protein autoubiquitination / mitotic spindle assembly checkpoint signaling / ubiquitin binding / kinetochore ...bub1-bub3 complex / Inactivation of APC/C via direct inhibition of the APC/C complex / mitotic DNA integrity checkpoint signaling / distributive segregation / mitotic checkpoint complex / meiotic sister chromatid cohesion, centromeric / positive regulation of protein autoubiquitination / mitotic spindle assembly checkpoint signaling / ubiquitin binding / kinetochore / cell division / nucleoplasm / nucleus
Similarity search - Function
N-terminal domain of TfIIb - #40 / 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 / N-terminal domain of TfIIb / Other non-globular ...N-terminal domain of TfIIb - #40 / 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 / N-terminal domain of TfIIb / Other non-globular / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Special / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Spindle assembly checkpoint protein BUB3 / Spindle assembly checkpoint component MAD3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.3Aug 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: Spindle assembly checkpoint component
C: Cell cycle arrest protein
D: Spindle assembly checkpoint component
E: Cell cycle arrest protein
F: Spindle assembly checkpoint component
G: Cell cycle arrest protein
H: Spindle assembly checkpoint component


Theoretical massNumber of molelcules
Total (without water)180,2408
Polymers180,2408
Non-polymers00
Water00
1
A: Cell cycle arrest protein
B: Spindle assembly checkpoint component


Theoretical massNumber of molelcules
Total (without water)45,0602
Polymers45,0602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-12 kcal/mol
Surface area15840 Å2
MethodPISA
2
C: Cell cycle arrest protein
D: Spindle assembly checkpoint component


Theoretical massNumber of molelcules
Total (without water)45,0602
Polymers45,0602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-12 kcal/mol
Surface area16300 Å2
MethodPISA
3
E: Cell cycle arrest protein
F: Spindle assembly checkpoint component


Theoretical massNumber of molelcules
Total (without water)45,0602
Polymers45,0602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-11 kcal/mol
Surface area15730 Å2
MethodPISA
4
G: Cell cycle arrest protein
H: Spindle assembly checkpoint component


Theoretical massNumber of molelcules
Total (without water)45,0602
Polymers45,0602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-11 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.352, 173.335, 90.019
Angle α, β, γ (deg.)90.00, 95.30, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a single heterodimer composed of Bub3 and the Mad3 GLEBS peptide. There are 4 heterodimers in the asymmetric unit.

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Components

#1: Protein
Cell cycle arrest protein


Mass: 38483.492 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BUB3, YOR026W, OR26.16 / Plasmid: pET-Duet (Novagen) / Production host: Escherichia coli (E. coli) / References: UniProt: P26449
#2: Protein
Spindle assembly checkpoint component / Mitotic MAD3 protein


Mass: 6576.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MAD3, YJL013C, J1341 / Plasmid: pET-Duet (Novagen) / Production host: Escherichia coli (E. coli) / References: UniProt: P47074

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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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17% PEG 4K 10% isopropanol 100 mM HEPES, pH 7.5, 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: 1.1807 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1807 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 40970 / % possible obs: 95.2 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 1.9 / % possible all: 76.1

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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: 2.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2673 1813 Random
Rwork0.2381 --
all0.242 35978 -
obs0.242 35978 -
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11816 0 0 0 11816
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.51202
X-RAY DIFFRACTIONc_bond_d0.008126
X-RAY DIFFRACTIONc_dihedral_angle_d25.99392
X-RAY DIFFRACTIONc_improper_angle_d0.81903

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