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- PDB-9j5k: Pathogen effector forms a phosphatase holoenzyme complex with hos... -

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Entry
Database: PDB / ID: 9j5k
TitlePathogen effector forms a phosphatase holoenzyme complex with host core enzyme to promote disease
Components
  • RxLR effector protein PSR2
  • Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform
  • Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
  • random substrate
KeywordsPLANT PROTEIN / pathogen / PP2A core enzyme / virulent function / susceptibility
Function / homology
Function and homology information


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 / peptidyl-threonine dephosphorylation / INTAC complex / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / FAR/SIN/STRIPAK complex / Regulation of glycolysis by fructose 2,6-bisphosphate 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 / peptidyl-threonine dephosphorylation / 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 / 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 / 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 / negative regulation of epithelial to mesenchymal transition / Co-inhibition by CTLA4 / Platelet sensitization by LDL / protein dephosphorylation / protein-serine/threonine phosphatase / negative regulation of glycolytic process through fructose-6-phosphate / ERK/MAPK targets / mesoderm development / protein serine/threonine phosphatase activity / vascular endothelial cell response to oscillatory fluid shear stress / 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 / DARPP-32 events / chromosome, centromeric region / 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) / phosphoprotein phosphatase activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / protein tyrosine phosphatase activity / EML4 and NUDC in mitotic spindle formation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Resolution of Sister Chromatid Cohesion / meiotic cell cycle / 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 / Negative regulation of MAPK pathway / Cyclin D associated events in G1 / Separation of Sister Chromatids / Regulation of TP53 Degradation / peroxisome / mitotic cell cycle / host cell / microtubule cytoskeleton / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / intracellular signal transduction / membrane raft / protein heterodimerization activity / synapse / chromatin / mitochondrion / extracellular exosome / extracellular region / metal ion binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / RXLR phytopathogen effector protein / RXLR phytopathogen effector protein, Avirulence activity / Effector PexRD54, WY-domain / : / : / HEAT repeat / HEAT repeat / : / PPP2R1A-like HEAT repeat ...: / RXLR phytopathogen effector protein / RXLR phytopathogen effector protein, Avirulence activity / Effector PexRD54, WY-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 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
: / RxLR effector protein PSR2 / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform
Similarity search - Component
Biological speciesHomo sapiens (human)
Phytophthora sojae (eukaryote)
Arabidopsis thaliana (thale cress)
Peptidiphaga (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsWang, J.L. / Wang, Y.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Pathogen effector forms a phosphatase holoenzyme complex with host core enzyme to promote disease
Authors: Wang, J.L. / Wang, Y.L.
History
DepositionAug 12, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
B: RxLR effector protein PSR2
A: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform
X: random substrate
F: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
E: RxLR effector protein PSR2
D: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform
Y: random substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,74712
Polymers353,5278
Non-polymers2204
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / PP2A-alpha / Replication protein C / RP-C


Mass: 35635.168 Da / Num. of mol.: 2
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
#2: Protein RxLR effector protein PSR2 / Avirulence homolog protein 146 / Suppressor of RNA silencing protein 2


Mass: 74706.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora sojae (eukaryote) / Gene: PSR2, Avh146 / Production host: Escherichia coli (E. coli) / References: UniProt: E0W4V5
#3: Protein Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform / AtA beta / PP2A / subunit A / beta isoform


Mass: 65666.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PP2AA2, DF1, At3g25800, K13N2.14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38950
#4: Protein/peptide random substrate


Mass: 754.773 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Peptidiphaga (bacteria)
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PSR2-PDF1-PPP2CA-random substrate / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Phytophthora sojae (eukaryote)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 156653 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00319402
ELECTRON MICROSCOPYf_angle_d0.63426576
ELECTRON MICROSCOPYf_dihedral_angle_d6.7782882
ELECTRON MICROSCOPYf_chiral_restr0.0413222
ELECTRON MICROSCOPYf_plane_restr0.0053474

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