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- PDB-8uwb: Crystal structure of PP2A PPP2R1A-PPP2CA-PPP2R5E phosphatase. -

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Basic information

Entry
Database: PDB / ID: 8uwb
TitleCrystal structure of PP2A PPP2R1A-PPP2CA-PPP2R5E phosphatase.
Components
  • Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform
  • Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
  • Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
KeywordsCELL CYCLE / PP2A / protein phosphatase / Serine/threonine-protein phosphatase 2A / B56epsilon
Function / homology
Function and homology information


meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / MASTL Facilitates Mitotic Progression / regulation of meiotic cell cycle process involved in oocyte maturation / mitotic sister chromatid separation / protein phosphatase type 2A complex / protein serine/threonine phosphatase complex / meiotic sister chromatid cohesion, centromeric ...meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / MASTL Facilitates Mitotic Progression / regulation of meiotic cell cycle process involved in oocyte maturation / mitotic sister chromatid separation / protein phosphatase type 2A complex / protein serine/threonine phosphatase complex / meiotic sister chromatid cohesion, centromeric / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / FAR/SIN/STRIPAK complex / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / positive regulation of microtubule binding / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / female meiotic nuclear division / GABA receptor binding / protein antigen binding / protein phosphatase regulator activity / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Initiation of Nuclear Envelope (NE) Reformation / ERKs are inactivated / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / 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 / regulation of growth / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of epithelial to mesenchymal transition / negative regulation of glycolytic process through fructose-6-phosphate / CTLA4 inhibitory signaling / Platelet sensitization by LDL / positive regulation of NLRP3 inflammasome complex assembly / protein serine/threonine phosphatase activity / myosin phosphatase activity / regulation of cell differentiation / protein-serine/threonine phosphatase / ERK/MAPK targets / T cell homeostasis / protein phosphatase activator activity / regulation of G1/S transition of mitotic cell cycle / mesoderm development / phosphoprotein phosphatase activity / chromosome, centromeric region / DARPP-32 events / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lateral plasma membrane / negative regulation of hippo signaling / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / EML4 and NUDC in mitotic spindle formation / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / protein dephosphorylation / AURKA Activation by TPX2 / protein tyrosine phosphatase activity / meiotic cell cycle / chromosome segregation / RHO GTPases Activate Formins / response to lead ion / RAF activation / regulation of protein phosphorylation / Spry regulation of FGF signaling / tau protein binding / positive regulation of protein serine/threonine kinase activity / PKR-mediated signaling / Degradation of beta-catenin by the destruction complex / spindle pole / Negative regulation of MAPK pathway / Separation of Sister Chromatids / Cyclin D associated events in G1 / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / Regulation of TP53 Degradation / mitotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein-containing complex assembly / intracellular signal transduction / neuron projection / protein heterodimerization activity / membrane raft / neuronal cell body / glutamatergic synapse / dendrite / synapse / signal transduction / mitochondrion / extracellular exosome
Similarity search - Function
Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / : / : / HEAT repeat / HEAT repeat / PPP2R1A-like HEAT repeat / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase ...Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / : / : / HEAT repeat / HEAT repeat / PPP2R1A-like HEAT repeat / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / HEAT repeat profile. / HEAT, type 2 / HEAT repeats / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
: / Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsWachter, F. / Nowak, R.P. / Fischer, E.S.
Funding support United States, 6items
OrganizationGrant numberCountry
Other privateASH Scholar Award United States
Other privateClaudia Adams Barr Award
Other privateWipe Out Kids Cancer
Other privatePedals for Pediatrics
Other privateBCH Faculty Development Award
The Mark FoundationMark Foundation Emerging Leaders Award United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural characterization of methylation-independent PP2A assembly guides alphafold2Multimer prediction of family-wide PP2A complexes.
Authors: Wachter, F. / Nowak, R.P. / Ficarro, S. / Marto, J. / Fischer, E.S.
History
DepositionNov 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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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 catalytic subunit alpha isoform
B: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform
C: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
D: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
E: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform
F: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,60510
Polymers322,3856
Non-polymers2204
Water00
1
A: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
B: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform
C: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,3025
Polymers161,1923
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-35 kcal/mol
Surface area55300 Å2
MethodPISA
2
D: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
E: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform
F: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,3025
Polymers161,1923
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-27 kcal/mol
Surface area54730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.839, 92.597, 134.657
Angle α, β, γ (deg.)83.770, 72.460, 73.460
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform


Mass: 68002.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MDWSHPQFEKSAVDENLYFQGGGR constitutes TEV cleavable Strep II tag used in affinity purifications.
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2CA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P67775
#2: Protein Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform / PP2A B subunit isoform B'-epsilon / PP2A B subunit isoform B56-epsilon / PP2A B subunit isoform ...PP2A B subunit isoform B'-epsilon / PP2A B subunit isoform B56-epsilon / PP2A B subunit isoform PR61-epsilon / PP2A B subunit isoform R5-epsilon


Mass: 54770.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: the N and C terminus is not visible in electron density and not modeled in.
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R5E / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q16537
#3: Protein Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform


Mass: 38420.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Tev cleavable Flag tag is used for purification. Flag-TEVsite: MDYKDDDDKSAVDENLYFQGGGR
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R1A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P30153
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
Has ligand of interestN

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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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.77 / Details: 23% (w/v) PEG 20k, 0.1 M BIS-TRIS pH 5.77

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 3.15→128.4 Å / Num. obs: 62227 / % possible obs: 96.42 % / Redundancy: 7.4 % / Biso Wilson estimate: 107.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.06023 / Rrim(I) all: 0.1655 / Net I/σ(I): 9.16
Reflection shellResolution: 3.15→3.263 Å / Redundancy: 0.82 % / Rmerge(I) obs: 2.011 / Mean I/σ(I) obs: 0.82 / Num. unique obs: 5795 / CC1/2: 0.397 / Rpim(I) all: 0.821 / Rrim(I) all: 2.177 / % possible all: 90.61

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→128.36 Å / SU ML: 0.5847 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.5509
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2629 3053 4.95 %
Rwork0.2205 58670 -
obs0.2227 61723 96.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 117.22 Å2
Refinement stepCycle: LAST / Resolution: 3.15→128.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20847 0 4 0 20851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002121293
X-RAY DIFFRACTIONf_angle_d0.504528864
X-RAY DIFFRACTIONf_chiral_restr0.03723283
X-RAY DIFFRACTIONf_plane_restr0.00393711
X-RAY DIFFRACTIONf_dihedral_angle_d4.11062808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.20.48751030.44642516X-RAY DIFFRACTION88.84
3.2-3.250.43461430.39782513X-RAY DIFFRACTION92.32
3.25-3.310.40091240.35672576X-RAY DIFFRACTION92.43
3.31-3.370.37751150.31742728X-RAY DIFFRACTION97.87
3.37-3.430.37361440.29272692X-RAY DIFFRACTION98.03
3.43-3.50.31271280.29182726X-RAY DIFFRACTION97.94
3.5-3.580.34921400.29462690X-RAY DIFFRACTION97.38
3.58-3.660.37751350.29512740X-RAY DIFFRACTION98.06
3.66-3.750.33971360.28142691X-RAY DIFFRACTION97.58
3.75-3.860.3581400.2642700X-RAY DIFFRACTION97.29
3.86-3.970.31011250.23962722X-RAY DIFFRACTION97.67
3.97-4.10.2791530.2162660X-RAY DIFFRACTION97.23
4.1-4.240.24031460.19842677X-RAY DIFFRACTION96.81
4.24-4.410.24151720.19342699X-RAY DIFFRACTION97.42
4.41-4.610.22851600.19722598X-RAY DIFFRACTION96
4.61-4.860.20631360.1782610X-RAY DIFFRACTION94.3
4.86-5.160.24051170.18762710X-RAY DIFFRACTION97.52
5.16-5.560.24921290.20922741X-RAY DIFFRACTION98.42
5.56-6.120.24451330.22642724X-RAY DIFFRACTION98.48
6.12-7.010.29131520.222690X-RAY DIFFRACTION97.5
7.01-8.830.22261570.19762651X-RAY DIFFRACTION96.73
8.83-128.360.20741650.16982616X-RAY DIFFRACTION95.53
Refinement TLS params.Method: refined / Origin x: -31.6401770466 Å / Origin y: -43.4646384379 Å / Origin z: -32.2763576472 Å
111213212223313233
T0.650659319944 Å20.01925616931 Å20.0146326860696 Å2-0.60592020297 Å2-0.0718840397366 Å2--0.853771475346 Å2
L0.153439518572 °2-0.0347132733987 °2-0.144070745478 °2-0.224982462662 °2-0.0641842175187 °2--0.835175547674 °2
S-0.0856846248302 Å °-0.0114751161226 Å °0.0565903107289 Å °0.040495111158 Å °0.00769454242542 Å °0.0805757853995 Å °0.14214841693 Å °-0.136019715134 Å °0.0724372654324 Å °
Refinement TLS groupSelection details: all

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