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- EMDB-48224: CryoEM structure of the Protein Phosphatase 2A (Abeta-B56gamma-Ca... -

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Basic information

Entry
Database: EMDB / ID: EMD-48224
TitleCryoEM structure of the Protein Phosphatase 2A (Abeta-B56gamma-Calpha) holoenzyme complex
Map data
Sample
  • Complex: Heterotrimer complex of the PP2A Abeta-B56gamma-Calpha holoenzyme
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
    • Protein or peptide: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
  • Ligand: MANGANESE (II) ION
KeywordsPhosphatase / Complex / Holoenzyme / Heterotrimer / SIGNALING PROTEIN / HYDROLASE
Function / homology
Function and homology information


Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / apoptotic process involved in morphogenesis / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / protein serine/threonine phosphatase complex / peptidyl-threonine dephosphorylation / meiotic sister chromatid cohesion, centromeric ...Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / apoptotic process involved in morphogenesis / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / protein serine/threonine phosphatase complex / peptidyl-threonine dephosphorylation / meiotic sister chromatid cohesion, centromeric / INTAC complex / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / FAR/SIN/STRIPAK complex / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / meiotic sister chromatid cohesion / protein phosphatase regulator activity / GABA receptor binding / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / ERKs are inactivated / Initiation of Nuclear Envelope (NE) Reformation / 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 / RNA polymerase II transcription initiation surveillance / Co-stimulation by CD28 / regulation of growth / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of epithelial to mesenchymal transition / Co-inhibition by CTLA4 / Platelet sensitization by LDL / protein-serine/threonine phosphatase / negative regulation of glycolytic process through fructose-6-phosphate / positive regulation of NLRP3 inflammasome complex assembly / ERK/MAPK targets / mesoderm development / protein serine/threonine phosphatase activity / vascular endothelial cell response to oscillatory fluid shear stress / T cell homeostasis / regulation of cell differentiation / regulation of G1/S transition of mitotic cell cycle / regulation of microtubule polymerization / phosphoprotein phosphatase activity / protein phosphatase activator activity / chromosome, centromeric region / DARPP-32 events / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of hippo signaling / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Cyclin A/B1/B2 associated events during G2/M transition / protein dephosphorylation / spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein tyrosine phosphatase activity / Resolution of Sister Chromatid Cohesion / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Spry regulation of FGF signaling / meiotic cell cycle / DNA damage response, signal transduction by p53 class mediator / Degradation of beta-catenin by the destruction complex / RHO GTPases Activate Formins / RAF activation / negative regulation of canonical Wnt signaling pathway / PKR-mediated signaling / tau protein binding / response to lead ion / Negative regulation of MAPK pathway / Cyclin D associated events in G1 / Separation of Sister Chromatids / Regulation of TP53 Degradation / spindle pole / mitotic cell cycle / microtubule cytoskeleton / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / proteasome-mediated ubiquitin-dependent protein catabolic process / intracellular signal transduction / membrane raft / protein heterodimerization activity / negative regulation of cell population proliferation / synapse / chromatin / Golgi apparatus / signal transduction / mitochondrion / extracellular exosome / nucleoplasm / metal ion binding / nucleus / membrane / plasma membrane / cytosol
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. ...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 beta isoform / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsDay A / Taylor D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Structure / Year: 2025
Title: Regulatory mechanisms of PP2A complex assembly driven by physicochemical differences in A-subunit isoforms.
Authors: Alexander Day / Wei Huang / Daniel Leonard / Caitlin M O'Connor / Goutham Narla / Derek J Taylor /
Abstract: Protein phosphatase 2A (PP2A) is crucial for regulating cellular pathways, with its holoenzyme assembly affecting enzyme function and substrate selection. The PP2A holoenzyme comprises scaffold A-, ...Protein phosphatase 2A (PP2A) is crucial for regulating cellular pathways, with its holoenzyme assembly affecting enzyme function and substrate selection. The PP2A holoenzyme comprises scaffold A-, regulatory B-, and catalytic C-subunits, each with various isoforms. Here, we examine structural and biochemical characteristics of the A-subunit isoforms (Aα and Aβ) and identify different biophysical properties that may promote distinct PP2A functions. Our molecular dynamics simulations and cryo-EM analyses define structural differences in the isoforms that reside primarily at the N-terminus of the A-subunit where it interfaces with regulatory B-subunits. Kinetic analyses show Aβ has a lower binding affinity in complexes with B56 subunits and exhibits unique aggregative properties as a monomeric protein. These findings suggest that the different physicochemical properties between A-subunit isoforms are key to PP2A holoenzyme assembly and function. We predict that the Aβ serves as a reservoir, ensuring that serine-threonine phosphatase activity is maintained during high regulatory demand.
History
DepositionDec 9, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48224.png

Downloads & links

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Map

FileDownload / File: emd_48224.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 270.848 Å		1.06 Å/pix.
x 256 pix.
= 270.848 Å		1.06 Å/pix.
x 256 pix.
= 270.848 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.154
Minimum - Maximum-0.34668824 - 0.63051116
Average (Standard dev.)-0.00017686661 (±0.01879184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 270.848 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_48224_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48224_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Heterotrimer complex of the PP2A Abeta-B56gamma-Calpha holoenzyme

EntireName: Heterotrimer complex of the PP2A Abeta-B56gamma-Calpha holoenzyme
Components
  • Complex: Heterotrimer complex of the PP2A Abeta-B56gamma-Calpha holoenzyme
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
    • Protein or peptide: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: Heterotrimer complex of the PP2A Abeta-B56gamma-Calpha holoenzyme

SupramoleculeName: Heterotrimer complex of the PP2A Abeta-B56gamma-Calpha holoenzyme
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 156 KDa

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Macromolecule #1: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit...

MacromoleculeName: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.277227 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAGASELGTG PGAAGGDGDD SLYPIAVLID ELRNEDVQLR LNSIKKLSTI ALALGVERTR SELLPFLTDT IYDEDEVLLA LAEQLGNFT GLVGGPDFAH CLLPPLENLA TVEETVVRDK AVESLRQISQ EHTPVALEAY FVPLVKRLAS GDWFTSRTSA C GLFSVCYP ...String:
MAGASELGTG PGAAGGDGDD SLYPIAVLID ELRNEDVQLR LNSIKKLSTI ALALGVERTR SELLPFLTDT IYDEDEVLLA LAEQLGNFT GLVGGPDFAH CLLPPLENLA TVEETVVRDK AVESLRQISQ EHTPVALEAY FVPLVKRLAS GDWFTSRTSA C GLFSVCYP RASNAVKAEI RQQFRSLCSD DTPMVRRAAA SKLGEFAKVL ELDSVKSEIV PLFTSLASDE QDSVRLLAVE AC VSIAQLL SQDDLETLVM PTLRQAAEDK SWRVRYMVAD RFSELQKAMG PKITLNDLIP AFQNLLKDCE AEVRAAAAHK VKE LGENLP IEDRETIIMN QILPYIKELV SDTNQHVKSA LASVIMGLST ILGKENTIEH LLPLFLAQLK DECPDVRLNI ISNL DCVNE VIGIRQLSQS LLPAIVELAE DAKWRVRLAI IEYMPLLAGQ LGVEFFDEKL NSLCMAWLVD HVYAIREAAT NNLMK LVQK FGTEWAQNTI VPKVLVMAND PNYLHRMTTL FCINALSEAC GQEITTKQML PIVLKMAGDQ VANVRFNVAK SLQKIG PIL DTNALQGEVK PVLQKLGQDE DMDVKYFAQE AISVLALA

UniProtKB: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform

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Macromolecule #2: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit...

MacromoleculeName: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.144645 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLTCNKAGSR MVVDAANSNG PFQPVVLLHI RDVPPADQEK LFIQKLRQCC VLFDFVSDPL SDLKWKEVKR AALSEMVEYI THNRNVITE PIYPEVVHMF AVNMFRTLPP SSNPTGAEFD PEEDEPTLEA AWPHLQLVYE FFLRFLESPD FQPNIAKKYI D QKFVLQLL ...String:
MLTCNKAGSR MVVDAANSNG PFQPVVLLHI RDVPPADQEK LFIQKLRQCC VLFDFVSDPL SDLKWKEVKR AALSEMVEYI THNRNVITE PIYPEVVHMF AVNMFRTLPP SSNPTGAEFD PEEDEPTLEA AWPHLQLVYE FFLRFLESPD FQPNIAKKYI D QKFVLQLL ELFDSEDPRE RDFLKTTLHR IYGKFLGLRA YIRKQINNIF YRFIYETEHH NGIAELLEIL GSIINGFALP LK EEHKIFL LKVLLPLHKV KSLSVYHPQL AYCVVQFLEK DSTLTEPVVM ALLKYWPKTH SPKEVMFLNE LEEILDVIEP SEF VKIMEP LFRQLAKCVS SPHFQVAERA LYYWNNEYIM SLISDNAAKI LPIMFPSLYR NSKTHWNKTI HGLIYNALKL FMEM NQKLF DDCTQQFKAE KLKEKLKMKE REEAWVKIEN LAKANPQYTV YSQASTMSIP VAMETDGPLF EDVQMLRKTV KDEAH QAQK DPKKDRPLAR RKSELPQDPH TKKALEAHCR ADELASQDGR

UniProtKB: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform

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Macromolecule #3: Serine/threonine-protein phosphatase 2A catalytic subunit alpha i...

MacromoleculeName: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein-serine/threonine phosphatase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.636152 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDEKVFTKEL DQWIEQLNEC KQLSESQVKS LCEKAKEILT KESNVQEVRC PVTVCGDVHG QFHDLMELFR IGGKSPDTNY LFMGDYVDR GYYSVETVTL LVALKVRYRE RITILRGNHE SRQITQVYGF YDECLRKYGN ANVWKYFTDL FDYLPLTALV D GQIFCLHG ...String:
MDEKVFTKEL DQWIEQLNEC KQLSESQVKS LCEKAKEILT KESNVQEVRC PVTVCGDVHG QFHDLMELFR IGGKSPDTNY LFMGDYVDR GYYSVETVTL LVALKVRYRE RITILRGNHE SRQITQVYGF YDECLRKYGN ANVWKYFTDL FDYLPLTALV D GQIFCLHG GLSPSIDTLD HIRALDRLQE VPHEGPMCDL LWSDPDDRGG WGISPRGAGY TFGQDISETF NHANGLTLVS RA HQLVMEG YNWCHDRNVV TIFSAPNYCY RCGNQAAIME LDDTLKYSFL QFDPAPRRGE PHVTRRTPDY FL

UniProtKB: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform

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Macromolecule #4: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloride
20.0 mMC8H18N2O4SHEPES
1.0 mMC4H10O2S2DTT
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.32 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio map generated by CryoSparc
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 248454
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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