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- PDB-5swf: The structure of the PP2A B56 subunit double phosphorylated BubR1... -

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Basic information

Entry
Database: PDB / ID: 5swf
TitleThe structure of the PP2A B56 subunit double phosphorylated BubR1 complex
Components
  • Double phosphorylated 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 / meiotic sister chromatid cohesion / protein phosphatase regulator activity / outer kinetochore ...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 / meiotic sister chromatid cohesion / 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 / Co-stimulation by CD28 / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Co-inhibition by CTLA4 / 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 / APC-Cdc20 mediated degradation of Nek2A / Resolution of Sister Chromatid Cohesion / DNA damage response, signal transduction by p53 class mediator / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / RHO GTPases Activate Formins / 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 / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / ciliary basal body / negative regulation of cell population proliferation / cell division / protein serine kinase activity / apoptotic process / centrosome / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
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 / FOURIER SYNTHESIS / Resolution: 2.818 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
DepositionAug 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Sep 13, 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 1.4Oct 4, 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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,8292
Polymers42,8292
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-7 kcal/mol
Surface area16480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.307, 107.422, 117.719
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 / Fragment: UNP residues 62-411
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 Double phosphorylated BubR1


Mass: 1162.098 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.: 13 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.93 Å3/Da / Density % sol: 68.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.75 / Details: 8% PEG 8k, 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 S 6M / Detector: PIXEL / Date: Jul 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.818→39.511 Å / Num. obs: 16683 / % possible obs: 98.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.5
Reflection shellResolution: 2.82→2.97 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.894 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.686 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5k6S

5k6s


Resolution: 2.818→39.5 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.26
RfactorNum. reflection% reflection
Rfree0.2305 1664 9.97 %
Rwork0.2075 --
obs0.2099 16683 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.818→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2731 0 0 13 2744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022812
X-RAY DIFFRACTIONf_angle_d0.7343820
X-RAY DIFFRACTIONf_dihedral_angle_d13.6771040
X-RAY DIFFRACTIONf_chiral_restr0.023425
X-RAY DIFFRACTIONf_plane_restr0.005481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8184-2.90130.33731220.30331103X-RAY DIFFRACTION89
2.9013-2.99490.32121430.2951256X-RAY DIFFRACTION100
2.9949-3.1020.33381380.27471232X-RAY DIFFRACTION99
3.102-3.22610.31231340.27511234X-RAY DIFFRACTION99
3.2261-3.37280.25591390.23841260X-RAY DIFFRACTION100
3.3728-3.55060.28581370.23091255X-RAY DIFFRACTION99
3.5506-3.77290.26371400.21791235X-RAY DIFFRACTION99
3.7729-4.06390.21191390.20431260X-RAY DIFFRACTION99
4.0639-4.47230.1871370.17541268X-RAY DIFFRACTION99
4.4723-5.11830.19241390.17881273X-RAY DIFFRACTION99
5.1183-6.4440.22411420.20111292X-RAY DIFFRACTION99
6.444-39.51520.20531540.18731351X-RAY DIFFRACTION98

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