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- PDB-6ef4: Crystal structure of mouse PP2A Aalpha P179R mutant -

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Basic information

Entry
Database: PDB / ID: 6ef4
TitleCrystal structure of mouse PP2A Aalpha P179R mutant
ComponentsSerine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
KeywordsPROTEIN BINDING / PP2A / Aalpha
Function / homology
Function and homology information


Inhibition of replication initiation of damaged DNA by RB1/E2F1 / ERKs are inactivated / Initiation of Nuclear Envelope (NE) Reformation / Cyclin A/B1/B2 associated events during G2/M transition / Co-inhibition by CTLA4 / Beta-catenin phosphorylation cascade / Co-stimulation by CD28 / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Negative regulation of MAPK pathway / Spry regulation of FGF signaling ...Inhibition of replication initiation of damaged DNA by RB1/E2F1 / ERKs are inactivated / Initiation of Nuclear Envelope (NE) Reformation / Cyclin A/B1/B2 associated events during G2/M transition / Co-inhibition by CTLA4 / Beta-catenin phosphorylation cascade / Co-stimulation by CD28 / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / Regulation of TP53 Degradation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin D associated events in G1 / meiotic spindle elongation / RAF activation / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Degradation of beta-catenin by the destruction complex / Resolution of Sister Chromatid Cohesion / PKR-mediated signaling / regulation of meiotic cell cycle process involved in oocyte maturation / mitotic sister chromatid separation / protein phosphatase type 2A complex / DARPP-32 events / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / meiotic sister chromatid cohesion, centromeric / RHO GTPases Activate Formins / Separation of Sister Chromatids / FAR/SIN/STRIPAK complex / Platelet sensitization by LDL / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / ERK/MAPK targets / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / female meiotic nuclear division / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Regulation of PLK1 Activity at G2/M Transition / protein antigen binding / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / protein serine/threonine phosphatase activity / T cell homeostasis / chromosome, centromeric region / lateral plasma membrane / negative regulation of hippo signaling / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / chromosome segregation / protein heterodimerization activity / neuronal cell body / synapse / dendrite / glutamatergic synapse / nucleus / cytosol
Similarity search - Function
: / HEAT repeat / HEAT repeat / : / PPP2R1A-like HEAT repeat / HEAT repeat profile. / HEAT, type 2 / HEAT repeats / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant ...: / HEAT repeat / HEAT repeat / : / PPP2R1A-like HEAT repeat / HEAT repeat profile. / HEAT, type 2 / HEAT repeats / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsWang, Z. / Shen, G. / Xu, W.
CitationJournal: Cancer Res. / Year: 2019
Title: The Highly Recurrent PP2A A alpha-Subunit Mutation P179R Alters Protein Structure and Impairs PP2A Enzyme Function to Promote Endometrial Tumorigenesis.
Authors: Taylor, S.E. / O'Connor, C.M. / Wang, Z. / Shen, G. / Song, H. / Leonard, D. / Sangodkar, J. / LaVasseur, C. / Avril, S. / Waggoner, S. / Zanotti, K. / Armstrong, A.J. / Nagel, C. / Resnick, ...Authors: Taylor, S.E. / O'Connor, C.M. / Wang, Z. / Shen, G. / Song, H. / Leonard, D. / Sangodkar, J. / LaVasseur, C. / Avril, S. / Waggoner, S. / Zanotti, K. / Armstrong, A.J. / Nagel, C. / Resnick, K. / Singh, S. / Jackson, M.W. / Xu, W. / Haider, S. / DiFeo, A. / Narla, G.
History
DepositionAug 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform


Theoretical massNumber of molelcules
Total (without water)65,5101
Polymers65,5101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.523, 122.523, 160.963
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / PP2A subunit A isoform PR65-alpha / PP2A subunit A isoform R1-alpha


Mass: 65509.500 Da / Num. of mol.: 1 / Mutation: P179R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ppp2r1a / Production host: Escherichia coli (E. coli) / References: UniProt: Q76MZ3

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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: 4.61 Å3/Da / Density % sol: 73.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium malonate pH 7.0, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 17427 / % possible obs: 99.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.039 / Rrim(I) all: 0.094 / Χ2: 0.996 / Net I/σ(I): 7.3 / Num. measured all: 112094
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.4-3.56.313960.7270.4560.88998.7
3.5-3.616.614350.7910.3630.86999.90.8720.946
3.61-3.746.614200.8710.160.9921000.3860.419
3.74-3.896.614080.9410.1570.9261000.3790.411
3.89-4.076.614440.9630.1211.01799.90.2910.316
4.07-4.286.614210.9750.0911.0531000.2190.237
4.28-4.556.514580.9850.0671.1021000.1590.173
4.55-4.96.514390.9910.0511.0499.90.120.13
4.9-5.46.514520.9910.0491.04899.90.1150.125
5.4-6.176.414800.9930.0441.0531000.1030.112
6.17-7.786.214910.9980.0281.01699.60.0650.071
7.78-505.915830.9990.0170.93498.30.0370.041

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IAE

2iae


Resolution: 3.4→48.79 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.961 / SU B: 25.45 / SU ML: 0.383 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 884 5.1 %RANDOM
Rwork0.2187 ---
obs0.2196 16510 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 239.45 Å2 / Biso mean: 126.481 Å2 / Biso min: 73.41 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å20 Å2
2---1.08 Å20 Å2
3---2.15 Å2
Refinement stepCycle: final / Resolution: 3.4→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4465 0 0 0 4465
Num. residues----572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0124536
X-RAY DIFFRACTIONr_angle_refined_deg0.8451.6276155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2995571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9422.986221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.87815832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9621528
X-RAY DIFFRACTIONr_chiral_restr0.0820.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023294
LS refinement shellResolution: 3.399→3.487 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 54 -
Rwork0.319 1153 -
all-1207 -
obs--94.82 %

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