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- EMDB-48798: PP2A-B55 Holoenzyme with Eya3 -

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Basic information

Entry
Database: EMDB / ID: EMD-48798
TitlePP2A-B55 Holoenzyme with Eya3
Map data
Sample
  • Complex: PP2A-B55 and Eya3 complex
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform
    • Protein or peptide: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
    • Protein or peptide: Protein phosphatase EYA3
KeywordsSer/Thr phosphatase / complex / Myc stabilization / ONCOPROTEIN
Function / homology
Function and homology information


histone H2AXY142 phosphatase activity / regulation of chromosome segregation / 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 / regulation of hippo signaling / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / INTAC complex ...histone H2AXY142 phosphatase activity / regulation of chromosome segregation / 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 / regulation of hippo signaling / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / 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 / snRNA processing / regulation of growth / protein phosphatase regulator activity / protein antigen binding / GABA receptor binding / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / regulation of transcription elongation by RNA polymerase II / ERKs are inactivated / T cell homeostasis / 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 / Initiation of Nuclear Envelope (NE) Reformation / Co-stimulation by CD28 / RNA polymerase II transcription initiation surveillance / Disassembly of the destruction complex and recruitment of AXIN to the membrane / protein dephosphorylation / negative regulation of glycolytic process through fructose-6-phosphate / negative regulation of epithelial to mesenchymal transition / Co-inhibition by CTLA4 / Platelet sensitization by LDL / protein-serine/threonine phosphatase / response to ionizing radiation / ERK/MAPK targets / vascular endothelial cell response to oscillatory fluid shear stress / protein serine/threonine phosphatase activity / regulation of cell differentiation / regulation of microtubule polymerization / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / lateral plasma membrane / DARPP-32 events / chromosome, centromeric region / anatomical structure morphogenesis / negative regulation of hippo signaling / enzyme-substrate adaptor activity / Cyclin A/B1/B2 associated events during G2/M transition / spindle assembly / regulation of G1/S transition of mitotic cell cycle / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / visual perception / phosphoprotein phosphatase activity / protein-tyrosine-phosphatase / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Recruitment of mitotic centrosome proteins and complexes / protein tyrosine phosphatase activity / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / protein phosphatase 2A binding / AURKA Activation by TPX2 / positive regulation of DNA repair / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Resolution of Sister Chromatid Cohesion / chromosome segregation / negative regulation of canonical Wnt signaling pathway / RAF activation / RHO GTPases Activate Formins / meiotic cell cycle / Spry regulation of FGF signaling / PKR-mediated signaling / response to lead ion / Degradation of beta-catenin by the destruction complex / tau protein binding / spindle pole / microtubule cytoskeleton / Cyclin D associated events in G1 / double-strand break repair / Negative regulation of MAPK pathway / Separation of Sister Chromatids / Regulation of TP53 Degradation / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein-containing complex assembly / cell differentiation
Similarity search - Function
EYA domain / Eyes absent family / EYA domain superfamily / EYA domain, metazoan / Protein phosphatase 2A regulatory subunit PR55 / Protein phosphatase 2A regulatory subunit PR55, conserved site / Protein phosphatase 2A regulatory subunit PR55 signature 1. / Protein phosphatase 2A regulatory subunit PR55 signature 2. / : / : ...EYA domain / Eyes absent family / EYA domain superfamily / EYA domain, metazoan / Protein phosphatase 2A regulatory subunit PR55 / Protein phosphatase 2A regulatory subunit PR55, conserved site / Protein phosphatase 2A regulatory subunit PR55 signature 1. / Protein phosphatase 2A regulatory subunit PR55 signature 2. / : / : / : / PIK3R4-like, middle domain / 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, type 2 / HEAT repeat profile. / HEAT repeats / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / haloacid dehalogenase-like hydrolase / Metallo-dependent phosphatase-like / Armadillo-like helical / Armadillo-type fold / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / Protein phosphatase EYA3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsShi S / Alderman C / Huang W / Zhao R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM145289 United States
CitationJournal: J Biol Chem / Year: 2025
Title: Cryo-EM structures reveal the PP2A-B55α and Eya3 interaction that can be disrupted by a peptide inhibitor.
Authors: Shasha Shi / Xueni Li / Christopher Alderman / Lars Wick / Wei Huang / North Foulon / Lingdi Zhang / John Rossi / Wenxin Hu / Shouqing Cui / Hongjin Zheng / Derek J Taylor / Heide L Ford / Rui Zhao /
Abstract: We have previously shown that Eya3 recruits PP2A-B55α to dephosphorylate pT58 on Myc, increasing Myc stability and enhancing primary tumor growth of triple-negative breast cancer (TNBC). However, ...We have previously shown that Eya3 recruits PP2A-B55α to dephosphorylate pT58 on Myc, increasing Myc stability and enhancing primary tumor growth of triple-negative breast cancer (TNBC). However, the molecular details of how Eya3 recruits PP2A-B55α remain unclear. Here, we determined the cryo-EM structures of PP2A-B55α bound with Eya3, with an inhibitory peptide B55i, and in its unbound state. These studies demonstrate that Eya3 binds B55α through an extended peptide in the N-terminal domain of Eya3. The Eya3 peptide, PP2A-B55α substrates, and protein-peptide inhibitors including B55i bind to a similar area on the B55α surface, but the molecular details of the binding differ. We further demonstrated that the B55i peptide inhibits the B55α and Eya3 interaction in vitro. The B55i peptide expressed on a plasmid increases Myc pT58 and decreases Myc protein levels in TNBC cells, suggesting the potential of B55i or similar peptides as therapies for TNBC.
History
DepositionJan 24, 2025-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48798.png

Downloads & links

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Map

FileDownload / File: emd_48798.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 273.6 Å		0.86 Å/pix.
x 320 pix.
= 273.6 Å		0.86 Å/pix.
x 320 pix.
= 273.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.7409268 - 1.072759
Average (Standard dev.)0.00089949183 (±0.019216526)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 273.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_48798_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48798_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : PP2A-B55 and Eya3 complex

EntireName: PP2A-B55 and Eya3 complex
Components
  • Complex: PP2A-B55 and Eya3 complex
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform
    • Protein or peptide: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
    • Protein or peptide: Protein phosphatase EYA3

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Supramolecule #1: PP2A-B55 and Eya3 complex

SupramoleculeName: PP2A-B55 and Eya3 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 160 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 alpha isoform
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.95798 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GHMSLYPIAV LIDELRNEDV QLRLNSIKKL STIALALGVE RTRSELLPFL TDTIYDEDEV LLALAEQLGT FTTLVGGPEY VHCLLPPLE SLATVEETVV RDKAVESLRA ISHEHSPSDL EAHFVPLVKR LAGGDWFTSR TSACGLFSVC YPRVSSAVKA E LRQYFRNL ...String:
GHMSLYPIAV LIDELRNEDV QLRLNSIKKL STIALALGVE RTRSELLPFL TDTIYDEDEV LLALAEQLGT FTTLVGGPEY VHCLLPPLE SLATVEETVV RDKAVESLRA ISHEHSPSDL EAHFVPLVKR LAGGDWFTSR TSACGLFSVC YPRVSSAVKA E LRQYFRNL CSDDTPMVRR AAASKLGEFA KVLELDNVKS EIIPMFSNLA SDEQDSVRLL AVEACVNIAQ LLPQEDLEAL VM PTLRQAA EDKSWRVRYM VADKFTELQK AVGPEITKTD LVPAFQNLMK DCEAEVRAAA SHKVKEFCEN LSADCRENVI MSQ ILPCIK ELVSDANQHV KSALASVIMG LSPILGKDNT IEHLLPLFLA QLKDECPEVR LNIISNLDCV NEVIGIRQLS QSLL PAIVE LAEDAKWRVR LAIIEYMPLL AGQLGVEFFD EKLNSLCMAW LVDHVYAIRE AATSNLKKLV EKFGKEWAHA TIIPK VLAM SGDPNYLHRM TTLFCINVLS EVCGQDITTK HMLPTVLRMA GDPVANVRFN VAKSLQKIGP ILDNSTLQSE VKPILE KLT QDQDVDVKYF AQEALTVLSL A

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

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Macromolecule #2: Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit...

MacromoleculeName: Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.10134 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GHMGSAGAGG GNDIQWCFSQ VKGAVDDDVA EADIISTVEF NHSGELLATG DKGGRVVIFQ QEQENKIQSH SRGEYNVYST FQSHEPEFD YLKSLEIEEK INKIRWLPQK NAAQFLLSTN DKTIKLWKIS ERDKRPEGYN LKEEDGRYRD PTTVTTLRVP V FRPMDLMV ...String:
GHMGSAGAGG GNDIQWCFSQ VKGAVDDDVA EADIISTVEF NHSGELLATG DKGGRVVIFQ QEQENKIQSH SRGEYNVYST FQSHEPEFD YLKSLEIEEK INKIRWLPQK NAAQFLLSTN DKTIKLWKIS ERDKRPEGYN LKEEDGRYRD PTTVTTLRVP V FRPMDLMV EASPRRIFAN AHTYHINSIS INSDYETYLS ADDLRINLWH LEITDRSFNI VDIKPANMEE LTEVITAAEF HP NSCNTFV YSSSKGTIRL CDMRASALCD RHSKLFEEPE DPSNRSFFSE IISSISDVKF SHSGRYMMTR DYLSVKIWDL NME NRPVET YQVHEYLRSK LCSLYENDCI FDKFECCWNG SDSVVMTGSY NNFFRMFDRN TKRDITLEAS RENNKPRTVL KPRK VCASG KRKKDEISVD SLDFNKKILH TAWHPKENII AVATTNNLYI FQDKVN

UniProtKB: Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha 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: Homo sapiens (human)
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: Protein phosphatase EYA3

MacromoleculeName: Protein phosphatase EYA3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein-tyrosine-phosphatase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.718516 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEEEQDLPEQ PVKKAKMQES GEQTISQVSN PDVSDQKPET SSLASNLPMS EEIMTCTDYI PRSSNDYTSQ MYSAKPYAHI LSVPVSETA YPGQTQYQTL QQTQPYAVYP QATQTYGLPP FGALWPGMKP ESGLIQTPSP SQHSVLTCTT GLTTSQPSPA H YSYPIQAS ...String:
MEEEQDLPEQ PVKKAKMQES GEQTISQVSN PDVSDQKPET SSLASNLPMS EEIMTCTDYI PRSSNDYTSQ MYSAKPYAHI LSVPVSETA YPGQTQYQTL QQTQPYAVYP QATQTYGLPP FGALWPGMKP ESGLIQTPSP SQHSVLTCTT GLTTSQPSPA H YSYPIQAS STNASLISTS STIANIPAAA VASISNQDYP TYTILGQNQY QACYPSSSFG VTGQTNSDAE STTLAATTYQ SE KPSVMAP APAAQRLSSG DPSTSPSLSQ TTPSKDTDDQ SRKNMTSKNR GKRKADATSS QDSELERVFL WDLDETIIIF HSL LTGSYA QKYGKDPTVV IGSGLTMEEM IFEVADTHLF FNDLEECDQV HVEDVASDDN GQDLSNYSFS TDGFSGSGGS GSHG SSVGV QGGVDWMRKL AFRYRKVREI YDKHKSNVGG LLSPQRKEAL QRLRAEIEVL TDSWLGTALK SLLLIQSRKN CVNVL ITTT QLVPALAKVL LYGLGEIFPI ENIYSATKIG KESCFERIVS RFGKKVTYVV IGDGRDEEIA AKQHNMPFWR ITNHGD LVS LHQALELDFL

UniProtKB: Protein phosphatase EYA3

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.004 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 159895
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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