+Open data
-Basic information
Entry | Database: PDB / ID: 8u89 | ||||||
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Title | The structure of the PP2A-B56Delta holoenzyme mutant - E197K | ||||||
Components |
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Keywords | CELL CYCLE / complex / phosphatase | ||||||
Function / homology | Function and homology information meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / MASTL Facilitates Mitotic Progression / mitotic sister chromatid separation / regulation of meiotic cell cycle process involved in oocyte maturation / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / peptidyl-serine dephosphorylation ...meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / MASTL Facilitates Mitotic Progression / mitotic sister chromatid separation / regulation of meiotic cell cycle process involved in oocyte maturation / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / : / positive regulation of microtubule binding / negative regulation of tyrosine phosphorylation of STAT protein / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / female meiotic nuclear division / protein antigen binding / protein phosphatase regulator activity / ceramide metabolic process / GABA receptor binding / negative regulation of epithelial to mesenchymal transition / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Initiation of Nuclear Envelope (NE) Reformation / 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 / regulation of Wnt signaling pathway / Disassembly of the destruction complex and recruitment of AXIN to the membrane / regulation of growth / negative regulation of glycolytic process through fructose-6-phosphate / positive regulation of NLRP3 inflammasome complex assembly / myosin phosphatase activity / protein serine/threonine phosphatase activity / CTLA4 inhibitory signaling / Platelet sensitization by LDL / negative regulation of MAPK cascade / protein-serine/threonine phosphatase / negative regulation of peptidyl-threonine phosphorylation / regulation of cell differentiation / T cell homeostasis / ERK/MAPK targets / protein phosphatase activator activity / regulation of G1/S transition of mitotic cell cycle / regulation of DNA replication / phosphoprotein phosphatase activity / mesoderm development / chromosome, centromeric region / DARPP-32 events / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lateral plasma membrane / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / regulation of cell adhesion / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of protein dephosphorylation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / protein dephosphorylation / RNA splicing / meiotic cell cycle / response to organic substance / protein tyrosine phosphatase activity / chromosome segregation / RHO GTPases Activate Formins / response to lead ion / regulation of protein phosphorylation / Spry regulation of FGF signaling / RAF activation / tau protein binding / PKR-mediated signaling / Degradation of beta-catenin by the destruction complex / positive regulation of protein serine/threonine kinase activity / negative regulation of cell growth / spindle pole / Negative regulation of MAPK pathway / Separation of Sister Chromatids / Cyclin D associated events in G1 / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / Regulation of TP53 Degradation / mitotic cell cycle / nervous system development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein-containing complex assembly / neuron projection Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Wu, C.G. / Xing, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024 Title: B56δ long-disordered arms form a dynamic PP2A regulation interface coupled with global allostery and Jordan's syndrome mutations. Authors: Cheng-Guo Wu / Vijaya K Balakrishnan / Ronald A Merrill / Pankaj S Parihar / Kirill Konovolov / Yu-Chia Chen / Zhen Xu / Hui Wei / Ramya Sundaresan / Qiang Cui / Brian E Wadzinski / Mark R ...Authors: Cheng-Guo Wu / Vijaya K Balakrishnan / Ronald A Merrill / Pankaj S Parihar / Kirill Konovolov / Yu-Chia Chen / Zhen Xu / Hui Wei / Ramya Sundaresan / Qiang Cui / Brian E Wadzinski / Mark R Swingle / Alla Musiyenko / Wendy K Chung / Richard E Honkanen / Aussie Suzuki / Xuhui Huang / Stefan Strack / Yongna Xing / Abstract: Intrinsically disordered regions (IDR) and short linear motifs (SLiMs) play pivotal roles in the intricate signaling networks governed by phosphatases and kinases. B56δ (encoded by ) is a regulatory ...Intrinsically disordered regions (IDR) and short linear motifs (SLiMs) play pivotal roles in the intricate signaling networks governed by phosphatases and kinases. B56δ (encoded by ) is a regulatory subunit of protein phosphatase 2A (PP2A) with long IDRs that harbor a substrate-mimicking SLiM and multiple phosphorylation sites. De novo missense mutations in cause intellectual disabilities (ID), macrocephaly, Parkinsonism, and a broad range of neurological symptoms. Our single-particle cryo-EM structures of the PP2A-B56δ holoenzyme reveal that the long, disordered arms at the B56δ termini fold against each other and the holoenzyme core. This architecture suppresses both the phosphatase active site and the substrate-binding protein groove, thereby stabilizing the enzyme in a closed latent form with dual autoinhibition. The resulting interface spans over 190 Å and harbors unfavorable contacts, activation phosphorylation sites, and nearly all residues with ID-associated mutations. Our studies suggest that this dynamic interface is coupled to an allosteric network responsive to phosphorylation and altered globally by mutations. Furthermore, we found that ID mutations increase the holoenzyme activity and perturb the phosphorylation rates, and the severe variants significantly increase the mitotic duration and error rates compared to the normal variant. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8u89.cif.gz | 259.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u89.ent.gz | 202.8 KB | Display | PDB format |
PDBx/mmJSON format | 8u89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/8u89 ftp://data.pdbj.org/pub/pdb/validation_reports/u8/8u89 | HTTPS FTP |
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-Related structure data
Related structure data | 42018MC 8u1xC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 65378.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R1A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P30153 | ||
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#2: Protein | Mass: 70089.742 Da / Num. of mol.: 1 / Mutation: E197K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R5D / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q14738 | ||
#3: Protein | Mass: 35636.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2CA / Production host: Trichoplusia ni (cabbage looper) References: UniProt: P67775, protein-serine/threonine phosphatase | ||
#4: Chemical | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Protein Phosphatase 2A B56 Delta holoenzyme mutant - E197K Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: UltrAuFoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2200 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 49 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 276448 / Symmetry type: POINT | ||||||||||||||||||||||||
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