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- EMDB-42428: Protein Phosphatase 2A B55 subunit in complex with IER5 -

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Entry
Database: EMDB / ID: EMD-42428
TitleProtein Phosphatase 2A B55 subunit in complex with IER5
Map dataProtein Phosphatase 2A B55 subunit in complex with IER5
Sample
  • Complex: PP2A complex with B55 regulatory subunit bound by IER5
    • 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: Immediate early response gene 5 protein
  • Ligand: FE (III) ION
  • Ligand: ZINC ION
KeywordsPhosphatase / complex / SIGNALING PROTEIN
Function / homology
Function and homology information


positive regulation of cellular response to heat / regulation of chromosome segregation / meiotic spindle elongation / 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 / peptidyl-threonine dephosphorylation / regulation of meiotic cell cycle process involved in oocyte maturation / mitotic sister chromatid separation / MASTL Facilitates Mitotic Progression ...positive regulation of cellular response to heat / regulation of chromosome segregation / meiotic spindle elongation / 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 / peptidyl-threonine dephosphorylation / regulation of meiotic cell cycle process involved in oocyte maturation / mitotic sister chromatid separation / 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 / female meiotic nuclear division / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / 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 / 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 / RNA polymerase II transcription initiation surveillance / regulation of growth / Disassembly of the destruction complex and recruitment of AXIN to the membrane / protein dephosphorylation / negative regulation of epithelial to mesenchymal transition / Co-inhibition by CTLA4 / Platelet sensitization by LDL / protein-serine/threonine phosphatase / response to morphine / ERK/MAPK targets / negative regulation of glycolytic process through fructose-6-phosphate / mesoderm development / vascular endothelial cell response to oscillatory fluid shear stress / protein serine/threonine phosphatase activity / positive regulation of NLRP3 inflammasome complex assembly / T cell homeostasis / regulation of cell differentiation / regulation of microtubule polymerization / regulation of G1/S transition of mitotic cell cycle / chromosome, centromeric region / lateral plasma membrane / DARPP-32 events / enzyme-substrate adaptor activity / negative regulation of hippo signaling / Cyclin A/B1/B2 associated events during G2/M transition / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / spindle assembly / phosphoprotein phosphatase activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / 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 / protein phosphatase 2A binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / meiotic cell cycle / chromosome segregation / RAF activation / Spry regulation of FGF signaling / negative regulation of canonical Wnt signaling pathway / RHO GTPases Activate Formins / PKR-mediated signaling / Degradation of beta-catenin by the destruction complex / response to lead ion / tau protein binding / spindle pole / Cyclin D associated events in G1 / Negative regulation of MAPK pathway / Separation of Sister Chromatids / Regulation of TP53 Degradation / Regulation of PLK1 Activity at G2/M Transition / regulation of cell population proliferation / mitotic cell cycle / cellular response to heat / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / microtubule cytoskeleton / protein-containing complex assembly / neuron projection / intracellular signal transduction
Similarity search - Function
Immediate early response / Immediate early response protein (IER) / 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. / : / : / : / Phosphatase 2A Regulatory Subunit A, helical domain ...Immediate early response / Immediate early response protein (IER) / 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. / : / : / : / Phosphatase 2A Regulatory Subunit A, helical 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 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 / 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 / Immediate early response gene 5 protein
Similarity search - Component
Biological speciesSpodoptera frugiperda (fall armyworm) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsJones DTD / Cao R / Rawson SD / Blacklow SC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA220340 United States
CitationJournal: Cell Chem Biol / Year: 2025
Title: Molecular mechanism of PP2A/B55α phosphatase inhibition by IER5.
Authors: Ruili Cao / Daniel T D Jones / Li Pan / Annie Yang / Shumei Wang / Sathish K R Padi / Shaun Rawson / Jon C Aster / Stephen C Blacklow /
Abstract: PP2A serine/threonine phosphatases are heterotrimeric complexes that execute many essential physiologic functions. These activities are modulated by additional regulatory proteins, such as ARPP19, ...PP2A serine/threonine phosphatases are heterotrimeric complexes that execute many essential physiologic functions. These activities are modulated by additional regulatory proteins, such as ARPP19, FAM122A, and IER5. Here, we report the cryoelectron microscopy (cryo-EM) structure of a complex of PP2A/B55α with the N-terminal structured region of IER5 (IER5-N50), which occludes a surface on B55α used for substrate recruitment, and show that IER5-N50 inhibits PP2A/B55α catalyzed dephosphorylation of pTau in biochemical assays. Mutations of full-length IER5 that disrupt its PP2A/B55α interface interfere with co-immunoprecipitation of PP2A/B55α. IER5 antagonism of B55α in keratinocytes is required for expression of KRT1, a differentiation marker. Mini-IER5 composed of IER5-N50 and a nuclear localization sequence restores this activity in IER5 knockout cells. Using structural bioinformatics, we identify homology of IER5-N50 with SERTA (SEI-1, RBT-1, and TARA) domain containing proteins. These studies define the molecular basis of PP2A/B55α nuclear inhibition by IER5 and suggest a roadmap for selective pharmacologic modulation of PP2A/B55α complexes.
History
DepositionOct 19, 2023-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42428.png

Downloads & links

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Map

FileDownload / File: emd_42428.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationProtein Phosphatase 2A B55 subunit in complex with IER5
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 297. Å		0.83 Å/pix.
x 360 pix.
= 297. Å		0.83 Å/pix.
x 360 pix.
= 297. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.89121747 - 1.2246362
Average (Standard dev.)-0.0006465101 (±0.025100712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 297.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #2

Fileemd_42428_additional_1.map
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Additional map: #1

Fileemd_42428_additional_2.map
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Half map: Half Map B

Fileemd_42428_half_map_1.map
AnnotationHalf Map B
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Half map: Half Map A

Fileemd_42428_half_map_2.map
AnnotationHalf Map A
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Sample components

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Entire : PP2A complex with B55 regulatory subunit bound by IER5

EntireName: PP2A complex with B55 regulatory subunit bound by IER5
Components
  • Complex: PP2A complex with B55 regulatory subunit bound by IER5
    • 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: Immediate early response gene 5 protein
  • Ligand: FE (III) ION
  • Ligand: ZINC ION

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Supramolecule #1: PP2A complex with B55 regulatory subunit bound by IER5

SupramoleculeName: PP2A complex with B55 regulatory subunit bound by IER5
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Spodoptera frugiperda (fall armyworm)

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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: 68.065211 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH SAVDENLYFQ GGGRMAAADG DDSLYPIAVL IDELRNEDVQ LRLNSIKKLS TIALALGVER TRSELLPFLT DTIYDEDEV LLALAEQLGT FTTLVGGPEY VHCLLPPLES LATVEETVVR DKAVESLRAI SHEHSPSDLE AHFVPLVKRL A GGDWFTSR ...String:
MGSSHHHHHH SAVDENLYFQ GGGRMAAADG DDSLYPIAVL IDELRNEDVQ LRLNSIKKLS TIALALGVER TRSELLPFLT DTIYDEDEV LLALAEQLGT FTTLVGGPEY VHCLLPPLES LATVEETVVR DKAVESLRAI SHEHSPSDLE AHFVPLVKRL A GGDWFTSR TSACGLFSVC YPRVSSAVKA ELRQYFRNLC SDDTPMVRRA AASKLGEFAK VLELDNVKSE IIPMFSNLAS DE QDSVRLL AVEACVNIAQ LLPQEDLEAL VMPTLRQAAE DKSWRVRYMV ADKFTELQKA VGPEITKTDL VPAFQNLMKD CEA EVRAAA SHKVKEFCEN LSADCRENVI MSQILPCIKE LVSDANQHVK SALASVIMGL SPILGKDNTI EHLLPLFLAQ LKDE CPEVR LNIISNLDCV NEVIGIRQLS QSLLPAIVEL AEDAKWRVRL AIIEYMPLLA GQLGVEFFDE KLNSLCMAWL VDHVY AIRE AATSNLKKLV EKFGKEWAHA TIIPKVLAMS GDPNYLHRMT TLFCINVLSE VCGQDITTKH MLPTVLRMAG DPVANV RFN VAKSLQKIGP ILDNSTLQSE VKPILEKLTQ DQDVDVKYFA QEALTVLSLA

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: 51.762012 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAGAGGGNDI QWCFSQVKGA VDDDVAEADI ISTVEFNHSG ELLATGDKGG RVVIFQQEQE NKIQSHSRGE YNVYSTFQSH EPEFDYLKS LEIEEKINKI RWLPQKNAAQ FLLSTNDKTI KLWKISERDK RPEGYNLKEE DGRYRDPTTV TTLRVPVFRP M DLMVEASP ...String:
MAGAGGGNDI QWCFSQVKGA VDDDVAEADI ISTVEFNHSG ELLATGDKGG RVVIFQQEQE NKIQSHSRGE YNVYSTFQSH EPEFDYLKS LEIEEKINKI RWLPQKNAAQ FLLSTNDKTI KLWKISERDK RPEGYNLKEE DGRYRDPTTV TTLRVPVFRP M DLMVEASP RRIFANAHTY HINSISINSD YETYLSADDL RINLWHLEIT DRSFNIVDIK PANMEELTEV ITAAEFHPNS CN TFVYSSS KGTIRLCDMR ASALCDRHSK LFEEPEDPSN RSFFSEIISS ISDVKFSHSG RYMMTRDYLS VKIWDLNMEN RPV ETYQVH EYLRSKLCSL YENDCIFDKF ECCWNGSDSV VMTGSYNNFF RMFDRNTKRD ITLEASRENN KPRTVLKPRK VCAS GKRKK DEISVDSLDF NKKILHTAWH PKENIIAVAT TNNLYIFQDK VN

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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.259879 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDYKDDDDKS AVDENLYFQG GGRMDEKVFT KELDQWIEQL NECKQLSESQ VKSLCEKAKE ILTKESNVQE VRCPVTVCGD VHGQFHDLM ELFRIGGKSP DTNYLFMGDY VDRGYYSVET VTLLVALKVR YRERITILRG NHESRQITQV YGFYDECLRK Y GNANVWKY ...String:
MDYKDDDDKS AVDENLYFQG GGRMDEKVFT KELDQWIEQL NECKQLSESQ VKSLCEKAKE ILTKESNVQE VRCPVTVCGD VHGQFHDLM ELFRIGGKSP DTNYLFMGDY VDRGYYSVET VTLLVALKVR YRERITILRG NHESRQITQV YGFYDECLRK Y GNANVWKY FTDLFDYLPL TALVDGQIFC LHGGLSPSID TLDHIRALDR LQEVPHEGPM CDLLWSDPDD RGGWGISPRG AG YTFGQDI SETFNHANGL TLVSRAHQLV MEGYNWCHDR NVVTIFSAPN YCYRCGNQAA IMELDDTLKY SFLQFDPAPR RGE PHVTRR TPDYFL

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

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Macromolecule #4: Immediate early response gene 5 protein

MacromoleculeName: Immediate early response gene 5 protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.532818 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MDWSHPQFEK SAVDENLYFQ GGGRMEFKLE AHRIVSISLG KIYNSRVQRG GIKLHKNLLV SLVLRSARQV YLSD

UniProtKB: Immediate early response gene 5 protein

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Macromolecule #5: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: FE
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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.7 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66568
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationNumber classes: 4
FSC plot (resolution estimation)

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