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- EMDB-45292: PP2A:B55-Eya3 substrate complex -

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Basic information

Entry
Database: EMDB / ID: EMD-45292
TitlePP2A:B55-Eya3 substrate complex
Map dataPrimary Map, ChimeraX contour level
Sample
  • Complex: PP2A:B55-EYA3
    • 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: Eyes absent homolog 3
  • Ligand: FE (II) ION
  • Ligand: ZINC ION
KeywordsPP2A:B55 / Eya3 / substrate complex / HYDROLASE / HYDROLASE-SUBSTRATE complex
Function / homology
Function and homology information


regulation of chromosome segregation / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / 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 / peptidyl-threonine dephosphorylation ...regulation of chromosome segregation / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / 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 / peptidyl-threonine dephosphorylation / meiotic sister chromatid cohesion, centromeric / peptidyl-serine dephosphorylation / FAR/SIN/STRIPAK complex / : / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / female meiotic nuclear division / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / GABA receptor binding / protein phosphatase regulator activity / protein antigen binding / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / ERKs are inactivated / Initiation of Nuclear Envelope (NE) Reformation / 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 / regulation of growth / Disassembly of the destruction complex and recruitment of AXIN to the membrane / response to morphine / negative regulation of epithelial to mesenchymal transition / Co-inhibition by CTLA4 / protein serine/threonine phosphatase activity / response to ionizing radiation / Platelet sensitization by LDL / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / negative regulation of glycolytic process through fructose-6-phosphate / positive regulation of NLRP3 inflammasome complex assembly / ERK/MAPK targets / T cell homeostasis / mesoderm development / vascular endothelial cell response to oscillatory fluid shear stress / regulation of cell differentiation / regulation of G1/S transition of mitotic cell cycle / phosphoprotein phosphatase activity / chromosome, centromeric region / DARPP-32 events / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / anatomical structure morphogenesis / positive regulation of protein serine/threonine kinase activity / lateral plasma membrane / negative regulation of hippo signaling / enzyme-substrate adaptor activity / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Cyclin A/B1/B2 associated events during G2/M transition / spindle assembly / protein dephosphorylation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / protein tyrosine phosphatase activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / visual perception / protein-tyrosine-phosphatase / Recruitment of mitotic centrosome proteins and complexes / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / positive regulation of DNA repair / AURKA Activation by TPX2 / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / meiotic cell cycle / chromosome segregation / RHO GTPases Activate Formins / RAF activation / response to lead ion / Spry regulation of FGF signaling / PKR-mediated signaling / Degradation of beta-catenin by the destruction complex / tau protein binding
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. / : / : / 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 / haloacid dehalogenase-like hydrolase / 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: 2.7 Å
AuthorsPage R / Peti W / Padi S / Godek RJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM144379 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM144483 United States
CitationJournal: Nature / Year: 2024
Title: Cryo-EM structures of PP2A:B55-FAM122A and PP2A:B55-ARPP19.
Authors: Sathish K R Padi / Margaret R Vos / Rachel J Godek / James R Fuller / Thomas Kruse / Jamin B Hein / Jakob Nilsson / Matthew S Kelker / Rebecca Page / Wolfgang Peti /
Abstract: Progression through the cell cycle is controlled by regulated and abrupt changes in phosphorylation. Mitotic entry is initiated by increased phosphorylation of mitotic proteins, a process driven by ...Progression through the cell cycle is controlled by regulated and abrupt changes in phosphorylation. Mitotic entry is initiated by increased phosphorylation of mitotic proteins, a process driven by kinases, whereas mitotic exit is achieved by counteracting dephosphorylation, a process driven by phosphatases, especially PP2A:B55. Although the role of kinases in mitotic entry is well established, recent data have shown that mitosis is only successfully initiated when the counterbalancing phosphatases are also inhibited. Inhibition of PP2A:B55 is achieved by the intrinsically disordered proteins ARPP19 and FAM122A. Despite their critical roles in mitosis, the mechanisms by which they achieve PP2A:B55 inhibition is unknown. Here, we report the single-particle cryo-electron microscopy structures of PP2A:B55 bound to phosphorylated ARPP19 and FAM122A. Consistent with our complementary NMR spectroscopy studies, both intrinsically disordered proteins bind PP2A:B55, but do so in highly distinct manners, leveraging multiple distinct binding sites on B55. Our extensive structural, biophysical and biochemical data explain how substrates and inhibitors are recruited to PP2A:B55 and provide a molecular roadmap for the development of therapeutic interventions for PP2A:B55-related diseases.
History
DepositionJun 11, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45292.png

Downloads & links

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Map

FileDownload / File: emd_45292.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary Map, ChimeraX contour level
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 400 pix.
= 292. Å		0.73 Å/pix.
x 400 pix.
= 292. Å		0.73 Å/pix.
x 400 pix.
= 292. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0909
Minimum - Maximum-0.33333352 - 0.7488342
Average (Standard dev.)0.00022698574 (±0.015344195)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 292.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45292_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Cryosparc sharpened map

Fileemd_45292_additional_1.map
AnnotationCryosparc sharpened map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: Half Map A

Fileemd_45292_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_45292_half_map_2.map
AnnotationHalf Map B
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Sample components

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Entire : PP2A:B55-EYA3

EntireName: PP2A:B55-EYA3
Components
  • Complex: PP2A:B55-EYA3
    • 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: Eyes absent homolog 3
  • Ligand: FE (II) ION
  • Ligand: ZINC ION

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Supramolecule #1: PP2A:B55-EYA3

SupramoleculeName: PP2A:B55-EYA3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / Details: PP2A:B55 (PP2Aa-B55-PP2Ac) bound to EYA3 62-110
Molecular weightTheoretical: 158.652 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: Escherichia coli (E. coli)
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: 35.845375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GHMDEKVFTK ELDQWIEQLN ECKQLSESQV KSLCEKAKEI LTKESNVQEV RCPVTVCGDV HGQFHDLMEL FRIGGKSPDT NYLFMGDYV DRGYYSVETV TLLVALKVRY RERITILRGN HESRQITQVY GFYDECLRKY GNANVWKYFT DLFDYLPLTA L VDGQIFCL ...String:
GHMDEKVFTK ELDQWIEQLN ECKQLSESQV KSLCEKAKEI LTKESNVQEV RCPVTVCGDV HGQFHDLMEL FRIGGKSPDT NYLFMGDYV DRGYYSVETV TLLVALKVRY RERITILRGN HESRQITQVY GFYDECLRKY GNANVWKYFT DLFDYLPLTA L VDGQIFCL HGGLSPSIDT LDHIRALDRL QEVPHEGPMC DLLWSDPDDR GGWGISPRGA GYTFGQDISE TFNHANGLTL VS RAHQLVM EGYNWCHDRN VVTIFSAPNY CYRCGNQAAI MELDDTLKYS FLQFDPAPRR GEPHVTRRTP DYF(MLL)

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

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Macromolecule #4: Eyes absent homolog 3

MacromoleculeName: Eyes absent homolog 3 / 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: 5.950449 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GHMRSSNDYT SQMYSAKPYA HILSVPVSET AYPGQTQYQT LQQTQPYAVY EE

UniProtKB: Protein phosphatase EYA3

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Macromolecule #5: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 4607 / Average exposure time: 7.0 sec. / Average electron dose: 51.04 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8so0


Details: PP2A:B55-FAM122A
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Details: GSFSC resolution (tight & corrected) / Number images used: 107919
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9c7t:
PP2A:B55-Eya3 substrate complex

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