[English] 日本語
Yorodumi
- PDB-9j5i: Pathogen effector forms a phosphatase holoenzyme complex with hos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9j5i
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
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 speciesPhytophthora sojae (eukaryote)
Homo sapiens (human)
Arabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsWang, Y.L. / Wang, J.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)(31930065, 31725008, 22121003, 91940302, 32071444, 32071198, and 31630015 China
CitationJournal: To Be Published
Title: Pathogen effector forms a phosphatase holoenzyme complex with host core enzyme to promote disease
Authors: Wang, Y.L. / Wang, J.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)352,23710
Polymers352,0186
Non-polymers2204
Water00
1


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

-
Components

#1: 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
#2: 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
#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: 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 modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: ternary complex of PSR2-PDF1-PPP2CA / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Phytophthora sojae (eukaryote)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

-
Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143584 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00319676
ELECTRON MICROSCOPYf_angle_d0.59626949
ELECTRON MICROSCOPYf_dihedral_angle_d5.0042855
ELECTRON MICROSCOPYf_chiral_restr0.0393251
ELECTRON MICROSCOPYf_plane_restr0.0053513

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more