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- PDB-5k6s: The structure of the PP2A B56 subunit BubR1 complex -

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Basic information

Entry
Database: PDB / ID: 5k6s
TitleThe structure of the PP2A B56 subunit BubR1 complex
Components
  • BubR1
  • Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
KeywordsHydrolase / cell cycle / Phosphatase / Regulator / SLiM
Function / homology
Function and homology information


mitotic checkpoint complex / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / metaphase/anaphase transition of mitotic cell cycle / protein phosphatase regulator activity / outer kinetochore / protein localization to chromosome, centromeric region ...mitotic checkpoint complex / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / metaphase/anaphase transition of mitotic cell cycle / protein phosphatase regulator activity / outer kinetochore / protein localization to chromosome, centromeric region / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / Disassembly of the destruction complex and recruitment of AXIN to the membrane / CTLA4 inhibitory signaling / Platelet sensitization by LDL / mitotic spindle assembly checkpoint signaling / protein phosphatase activator activity / chromosome, centromeric region / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 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 / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / APC-Cdc20 mediated degradation of Nek2A / RHO GTPases Activate Formins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / RAF activation / Degradation of beta-catenin by the destruction complex / kinetochore / spindle / Negative regulation of MAPK pathway / Separation of Sister Chromatids / Regulation of TP53 Degradation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / proteasome-mediated ubiquitin-dependent protein catabolic process / non-specific serine/threonine protein kinase / protein kinase activity / negative regulation of cell population proliferation / phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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 / Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical ...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 / Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Protein kinase-like domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Mitotic checkpoint serine/threonine-protein kinase BUB1 beta / Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.794 Å
AuthorsPage, R. / Wang, X. / Bajaj, R. / Peti, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1R01NS091336 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098482 United States
CitationJournal: Structure / Year: 2016
Title: Expanding the PP2A Interactome by Defining a B56-Specific SLiM.
Authors: Wang, X. / Bajaj, R. / Bollen, M. / Peti, W. / Page, R.
History
DepositionMay 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
B: BubR1


Theoretical massNumber of molelcules
Total (without water)43,9322
Polymers43,9322
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-8 kcal/mol
Surface area17220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.231, 107.811, 117.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform / PP2A B subunit isoform B'-gamma / PP2A B subunit isoform B56-gamma / PP2A B subunit isoform PR61- ...PP2A B subunit isoform B'-gamma / PP2A B subunit isoform B56-gamma / PP2A B subunit isoform PR61-gamma / PP2A B subunit isoform R5-gamma / Renal carcinoma antigen NY-REN-29


Mass: 41667.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R5C, KIAA0044 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13362
#2: Protein/peptide BubR1


Mass: 2264.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O60566*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 4 Å3/Da / Density % sol: 69.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.75 / Details: 8% PEG 6K, 0.8 M HEPES, 0.8 M LiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.79→39.52 Å / Num. obs: 17235 / % possible obs: 98.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 81.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 16.8
Reflection shellResolution: 2.79→2.94 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.382 / % possible all: 93.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.5.17data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JAK

2jak


Resolution: 2.794→39.522 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2268 1715 10.01 %
Rwork0.1984 --
obs0.2013 17130 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.794→39.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2762 0 0 10 2772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022849
X-RAY DIFFRACTIONf_angle_d0.6863867
X-RAY DIFFRACTIONf_dihedral_angle_d12.8711063
X-RAY DIFFRACTIONf_chiral_restr0.023428
X-RAY DIFFRACTIONf_plane_restr0.004488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.794-2.87620.37131270.34421125X-RAY DIFFRACTION89
2.8762-2.9690.32061420.28341277X-RAY DIFFRACTION99
2.969-3.07510.29061410.26041271X-RAY DIFFRACTION100
3.0751-3.19820.25511420.24121276X-RAY DIFFRACTION99
3.1982-3.34370.26341410.22571262X-RAY DIFFRACTION97
3.3437-3.51990.25851430.20321288X-RAY DIFFRACTION100
3.5199-3.74020.26671420.20651288X-RAY DIFFRACTION100
3.7402-4.02880.23321450.19891301X-RAY DIFFRACTION100
4.0288-4.43370.20871440.17441298X-RAY DIFFRACTION98
4.4337-5.07410.20931450.17761300X-RAY DIFFRACTION100
5.0741-6.38850.22971480.19741335X-RAY DIFFRACTION99
6.3885-39.52630.1811550.17731394X-RAY DIFFRACTION98

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