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- EMDB-41604: Cryo-EM structure of the PP2A:B55-ARPP19 complex -

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Entry
Database: EMDB / ID: EMD-41604
TitleCryo-EM structure of the PP2A:B55-ARPP19 complex
Map dataRelion 3D auto refine full map. This map was used for Phenix real-space refinement of model coordinates and ADPs.
Sample
  • Complex: Quadruple complex of PP2A:B55 (PP2Aa:PP2Ac:B55) bound to thiophosphorylated ARPP19
    • 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: cAMP-regulated phosphoprotein 19
  • Ligand: FE (III) ION
  • Ligand: ZINC ION
KeywordsProtein Phosphatase 2A:B55 holoenzyme / ARPP19 inhibitor / cell cycle regulation / SIGNALING PROTEIN / HYDROLASE
Function / homology
Function and homology information


phosphatase inhibitor activity / regulation of chromosome segregation / meiotic spindle elongation / 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 / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / protein serine/threonine phosphatase complex ...phosphatase inhibitor activity / regulation of chromosome segregation / meiotic spindle elongation / 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 / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / protein serine/threonine phosphatase complex / regulation of meiotic cell cycle process involved in oocyte maturation / peptidyl-threonine dephosphorylation / mitotic sister chromatid separation / 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 / female meiotic nuclear division / 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 / protein antigen binding / ERKs are inactivated / 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 / Initiation of Nuclear Envelope (NE) Reformation / 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 / response to morphine / Co-inhibition by CTLA4 / protein phosphatase inhibitor activity / 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 / phosphoprotein phosphatase activity / regulation of microtubule polymerization / regulation of G1/S transition of mitotic cell cycle / lateral plasma membrane / chromosome, centromeric region / DARPP-32 events / enzyme-substrate adaptor activity / negative regulation of hippo signaling / potassium channel regulator activity / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein dephosphorylation / Cyclin A/B1/B2 associated events during G2/M transition / spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / positive regulation of gluconeogenesis / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / 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 / protein tyrosine phosphatase activity / Resolution of Sister Chromatid Cohesion / protein phosphatase 2A binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / AURKA Activation by TPX2 / positive regulation of D-glucose import / meiotic cell cycle / chromosome segregation / RHO GTPases Activate Formins / RAF activation / Spry regulation of FGF signaling / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / PKR-mediated signaling / response to lead ion / tau protein binding / G2/M transition of mitotic cell cycle / spindle pole / Negative regulation of MAPK pathway / Cyclin D associated events in G1 / Separation of Sister Chromatids / Regulation of TP53 Degradation / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle
Similarity search - Function
Endosulphine / cAMP-regulated phosphoprotein/endosulfine conserved region / 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 ...Endosulphine / cAMP-regulated phosphoprotein/endosulfine conserved region / 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 / 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 / cAMP-regulated phosphoprotein 19 / 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: 2.77 Å
AuthorsFuller JR / Padi SKR / Peti W / Page R
Funding support United States, 3 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)R01GM134683 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS124666 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
DepositionAug 13, 2023-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41604.png

Downloads & links

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Map

FileDownload / File: emd_41604.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRelion 3D auto refine full map. This map was used for Phenix real-space refinement of model coordinates and ADPs.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 352 pix.
= 291.104 Å		0.83 Å/pix.
x 352 pix.
= 291.104 Å		0.83 Å/pix.
x 352 pix.
= 291.104 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0075
Minimum - Maximum-0.014063554 - 0.037588034
Average (Standard dev.)-0.000012589108 (±0.00091936835)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 291.104 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41604_msk_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Additional map: Map version that was globally sharpened by a...

Fileemd_41604_additional_1.map
AnnotationMap version that was globally sharpened by a B-factor of -40.0 and filtered to local resolution by the implementation in Relion. This was used to guide manual model building.
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Relion 3D auto refine half map 1

Fileemd_41604_half_map_1.map
AnnotationRelion 3D auto refine half map 1
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Relion 3D auto refine half map 2

Fileemd_41604_half_map_2.map
AnnotationRelion 3D auto refine half map 2
Projections & Slices
AxesZYX

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Sample components

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Entire : Quadruple complex of PP2A:B55 (PP2Aa:PP2Ac:B55) bound to thiophos...

EntireName: Quadruple complex of PP2A:B55 (PP2Aa:PP2Ac:B55) bound to thiophosphorylated ARPP19
Components
  • Complex: Quadruple complex of PP2A:B55 (PP2Aa:PP2Ac:B55) bound to thiophosphorylated ARPP19
    • 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: cAMP-regulated phosphoprotein 19
  • Ligand: FE (III) ION
  • Ligand: ZINC ION

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Supramolecule #1: Quadruple complex of PP2A:B55 (PP2Aa:PP2Ac:B55) bound to thiophos...

SupramoleculeName: Quadruple complex of PP2A:B55 (PP2Aa:PP2Ac:B55) bound to thiophosphorylated ARPP19
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 165 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: 52.044289 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HMGSAGAGGG NDIQWCFSQV KGAVDDDVAE ADIISTVEFN HSGELLATGD KGGRVVIFQQ EQENKIQSHS RGEYNVYSTF QSHEPEFDY LKSLEIEEKI NKIRWLPQKN AAQFLLSTND KTIKLWKISE RDKRPEGYNL KEEDGRYRDP TTVTTLRVPV F RPMDLMVE ...String:
HMGSAGAGGG NDIQWCFSQV KGAVDDDVAE ADIISTVEFN HSGELLATGD KGGRVVIFQQ EQENKIQSHS RGEYNVYSTF QSHEPEFDY LKSLEIEEKI NKIRWLPQKN AAQFLLSTND KTIKLWKISE RDKRPEGYNL KEEDGRYRDP TTVTTLRVPV F RPMDLMVE ASPRRIFANA HTYHINSISI NSDYETYLSA DDLRINLWHL EITDRSFNIV DIKPANMEEL TEVITAAEFH PN SCNTFVY SSSKGTIRLC DMRASALCDR HSKLFEEPED PSNRSFFSEI ISSISDVKFS HSGRYMMTRD YLSVKIWDLN MEN RPVETY QVHEYLRSKL CSLYENDCIF DKFECCWNGS DSVVMTGSYN NFFRMFDRNT KRDITLEASR ENNKPRTVLK PRKV CASGK RKKDEISVDS LDFNKKILHT AWHPKENIIA VATTNNLYIF QDKVN

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: cAMP-regulated phosphoprotein 19

MacromoleculeName: cAMP-regulated phosphoprotein 19 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.620241 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GHMSAEVPEA ASAEEQKEME DKVTSPEKAE EAKLKARYPH LGQKPGGSDF LRKRLQKGQK YFD(2RX)GDYNMA KAKMKN KQL PTAAPDKTEV TGDHIPTPQD LPQRKPALVA SKLAG

UniProtKB: cAMP-regulated phosphoprotein 19

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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

Concentration1.2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
1.0 mMMnCl2manganese (II) chloride
20.0 mMC4H11NO3tris
0.5 mMC9H15O6PTCEP
0.125 %C32H58N2O8SCHAPSO

Details: CHAPSO was added only immediately prior to vitrification
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 70.0 e/Å2
Details: Camera was operated in CDS mode, with hardware binning of super-resolution pixels, writing movies with 62 frames
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.6 µm / Calibrated defocus min: 0.39 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000
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

Particle selectionNumber selected: 1170216
Startup modelType of model: OTHER
Details: Initial model was generated directly from particles images using the RELION 4.0.1 3D initial model algorithm
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number images used: 52934
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3dw8

source_name: PDB, initial_model_type: experimental model

6211

source_name: AlphaFold, initial_model_type: in silico model
DetailsIterating between manual refinement in Coot and automated real-space refinement in Phenix
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation
Output model

PDB-8ttb:
Cryo-EM structure of the PP2A:B55-ARPP19 complex

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