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- EMDB-45243: PP2A:B55-p107 substrate complex -

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Entry
Database: EMDB / ID: EMD-45243
TitlePP2A:B55-p107 substrate complex
Map dataPrimary Map NU-Refinment, Cryosparc, phenix
Sample
  • Complex: PP2A:B55-p107
    • 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: Retinoblastoma-like protein 1
  • Ligand: FE (II) ION
  • Ligand: ZINC ION
KeywordsPP2A:B55 / p107 / substrate complex / HYDROLASE / HYDROLASE-SUBSTRATE complex
Function / homology
Function and homology information


regulation of lipid kinase 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 / DRM complex / regulation of hippo signaling / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric ...regulation of lipid kinase 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 / DRM complex / regulation of hippo signaling / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / INTAC complex / protein serine/threonine phosphatase 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 / regulation of transcription elongation by RNA polymerase II / protein phosphatase regulator activity / protein antigen binding / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / 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 / 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 / Transcription of E2F targets under negative control by DREAM complex / RNA polymerase II transcription initiation surveillance / integrator complex / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of G1/S transition of mitotic cell cycle / protein dephosphorylation / negative regulation of glycolytic process through fructose-6-phosphate / negative regulation of cellular senescence / negative regulation of epithelial to mesenchymal transition / Co-inhibition by CTLA4 / Platelet sensitization by LDL / protein-serine/threonine phosphatase / G1/S-Specific Transcription / ERK/MAPK targets / vascular endothelial cell response to oscillatory fluid shear stress / regulation of cell differentiation / protein serine/threonine phosphatase activity / G0 and Early G1 / regulation of microtubule polymerization / positive regulation of NLRP3 inflammasome complex assembly / DARPP-32 events / chromosome, centromeric region / lateral plasma membrane / enzyme-substrate adaptor activity / negative regulation of hippo signaling / Cyclin A/B1/B2 associated events during G2/M transition / spindle assembly / phosphoprotein phosphatase activity / regulation of G1/S transition of mitotic cell cycle / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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 / Recruitment of NuMA to mitotic centrosomes / protein tyrosine phosphatase activity / Anchoring of the basal body to the plasma membrane / Mitotic Prometaphase / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / 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 / 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 / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / RHO GTPases Activate Formins / RAF activation / Spry regulation of FGF signaling / response to lead ion / PKR-mediated signaling / Degradation of beta-catenin by the destruction complex / tau protein binding / microtubule cytoskeleton / Cyclin D associated events in G1 / Negative regulation of MAPK pathway / Separation of Sister Chromatids / Regulation of TP53 Degradation / mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition
Similarity search - Function
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. / Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family ...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. / Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) / Domain of unknown function (DUF3452) / Retinoblastoma-associated protein A domain / Rb C-terminal domain / : / : / : / 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 / Metallo-dependent phosphatase-like / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / 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
Retinoblastoma-like protein 1 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 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 7, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45243.png

Downloads & links

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Map

FileDownload / File: emd_45243.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary Map NU-Refinment, Cryosparc, phenix
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 336 pix.
= 277.738 Å		0.83 Å/pix.
x 336 pix.
= 277.738 Å		0.83 Å/pix.
x 336 pix.
= 277.738 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8266 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0529
Minimum - Maximum-0.18718201 - 0.44349965
Average (Standard dev.)0.0004778152 (±0.0103719495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 277.7376 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45243_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_45243_half_map_1.map
AnnotationHalf_map_A
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_45243_half_map_2.map
AnnotationHalf_map_B
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Sample components

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Entire : PP2A:B55-p107

EntireName: PP2A:B55-p107
Components
  • Complex: PP2A:B55-p107
    • 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: Retinoblastoma-like protein 1
  • Ligand: FE (II) ION
  • Ligand: ZINC ION

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Supramolecule #1: PP2A:B55-p107

SupramoleculeName: PP2A:B55-p107 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: The PP2A:B55 complex (PP2Aa:B55:PP2Ac) bound to p107
Molecular weightTheoretical: 161.4 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: Retinoblastoma-like protein 1

MacromoleculeName: Retinoblastoma-like protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.716149 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GHMPMSPLMH PRVKEVRTDS GSLRRDMQPL SPISVHERYS SPTAGSAKRR LFGEDPPKEM LMDKIITEGT KLKIAPSS

UniProtKB: Retinoblastoma-like protein 1

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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
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / Number real images: 5007 / Average electron dose: 39.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.55 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2800783
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8so0

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0) / Number images used: 195950
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 / Overall B value: 60 / Target criteria: Cross-correlation coefficient
Output model

PDB-9c6b:
PP2A:B55-p107 substrate complex

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