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- EMDB-61147: Pathogen effector forms a phosphatase holoenzyme complex with hos... -

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Basic information

Entry
Database: EMDB / ID: EMD-61147
TitlePathogen effector forms a phosphatase holoenzyme complex with host core enzyme to promote disease
Map data
Sample
  • Complex: PSR2-PDF1-PPP2CA-trimer S2
    • Protein or peptide: RxLR effector protein PSR2
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform
    • Protein or peptide: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
  • Ligand: MANGANESE (II) ION
Keywordspathogen / PP2A core enzyme / virulent function / susceptibility / PLANT PROTEIN
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) / Arabidopsis thaliana (thale cress) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsWang YL / Wang JL
Funding support China, 1 items
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 YL / Wang JL
History
DepositionAug 13, 2024-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61147.png

Downloads & links

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Map

FileDownload / File: emd_61147.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 280 pix.
= 296.8 Å		1.06 Å/pix.
x 280 pix.
= 296.8 Å		1.06 Å/pix.
x 280 pix.
= 296.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-4.330405 - 6.10301
Average (Standard dev.)0.002080957 (±0.082087025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 296.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61147_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61147_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PSR2-PDF1-PPP2CA-trimer S2

EntireName: PSR2-PDF1-PPP2CA-trimer S2
Components
  • Complex: PSR2-PDF1-PPP2CA-trimer S2
    • Protein or peptide: RxLR effector protein PSR2
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform
    • Protein or peptide: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: PSR2-PDF1-PPP2CA-trimer S2

SupramoleculeName: PSR2-PDF1-PPP2CA-trimer S2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Phytophthora sojae (eukaryote)

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Macromolecule #1: RxLR effector protein PSR2

MacromoleculeName: RxLR effector protein PSR2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Phytophthora sojae (eukaryote)
Molecular weightTheoretical: 74.706656 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRLQCVVLFA ALTLVAATHA PPNVKTVLSA EQHDIPVKRL LRPGNPAGKE DEERGINFSS VPGFEKLANL LKPKPGLKKL LKWADAKKP PETVFTRLRL DKTGTQLFDN TDFPVWAAYT RSVAQTDSEA SAVMLKTLVS RYSDEVLSGM IAAAKKSSKT E SIATKLET ...String:
MRLQCVVLFA ALTLVAATHA PPNVKTVLSA EQHDIPVKRL LRPGNPAGKE DEERGINFSS VPGFEKLANL LKPKPGLKKL LKWADAKKP PETVFTRLRL DKTGTQLFDN TDFPVWAAYT RSVAQTDSEA SAVMLKTLVS RYSDEVLSGM IAAAKKSSKT E SIATKLET EQMRTWLAAK KTPDDMFLVF KLNKAGDDIL SSPLLSAWTN YMKLSNKENP KAQTTLIATM TKHYGDSGVS QI LAAARKS PATQSTAKRL EAEQVQLWLK KGRTPDDTFT LLSLDRAGDD LLASPQFNTW MKYINYYNKE NPDEKTTVLA KLM THFDDE ELTPILVVAR KVPSTESTAA KLQAEQFKNW LSADKSPEEA FTLLQLDKAG DDLLTNPQLT NWLKYTENFN LNKE INEQV TAIQVFRAQY VDDSRIANMV IAAEKVPNTQ AIAKRVEDEL FKGWTVVLNK PDDVFINLKL ETVGENVFES PLWSF YTKF LEKYNTANPG KEQTMISGLA RGYNDVTLTN MLLKAKEAPS TKTLATKLED ELVQYWLADK KLPDKLFGYL ELKESV DGI LTNPVFNVWL KYLNAFNDKA PVKKALMIDT LKSAFGDVAV SNMLFAAKKD PGTAKVAATL QTALLSKWVL EKKTPGQ VS AILKEGAGAD VSAKLLATYS AKFKVRWG

UniProtKB: RxLR effector protein PSR2

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Macromolecule #2: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit...

MacromoleculeName: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 65.666969 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSMIDEPLYP IAVLIDELKN DDIQLRLNSI RRLSTIARAL GEERTRKELI PFLSENNDDD DEVLLAMAEE LGVFIPYVGG VEYAHVLLP PLETLSTVEE TCVREKAVES LCRVGSQMRE SDLVDHFISL VKRLAAGEWF TARVSACGVF HIAYPSAPDM L KTELRSLY ...String:
MSMIDEPLYP IAVLIDELKN DDIQLRLNSI RRLSTIARAL GEERTRKELI PFLSENNDDD DEVLLAMAEE LGVFIPYVGG VEYAHVLLP PLETLSTVEE TCVREKAVES LCRVGSQMRE SDLVDHFISL VKRLAAGEWF TARVSACGVF HIAYPSAPDM L KTELRSLY TQLCQDDMPM VRRAAATNLG KFAATVESAH LKTDVMSMFE DLTQDDQDSV RLLAVEGCAA LGKLLEPQDC VQ HILPVIV NFSQDKSWRV RYMVANQLYE LCEAVGPEPT RTELVPAYVR LLRDNEAEVR IAAAGKVTKF CRILNPEIAI QHI LPCVKE LSSDSSQHVR SALASVIMGM APVLGKDATI EHLLPIFLSL LKDEFPDVRL NIISKLDQVN QVIGIDLLSQ SLLP AIVEL AEDRHWRVRL AIIEYIPLLA SQLGVGFFDD KLGALCMQWL QDKVHSIRDA AANNLKRLAE EFGPEWAMQH IVPQV LEMV NNPHYLYRMT ILRAVSLLAP VMGSEITCSK LLPVVMTASK DRVPNIKFNV AKVLQSLIPI VDQSVVEKTI RPGLVE LSE DPDVDVRFFA NQALQSIDNV MMSS

UniProtKB: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta 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: 35.635168 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDEKVFTKEL DQWIEQLNEC KQLSESQVKS LCEKAKEILT KESNVQEVRC PVTVCGDVHG QFHDLMELFR IGGKSPDTNY LFMGDYVNR GYYSVETVTL LVALKVRYRE RITILRGNHE SRQITQVYGF YDECLRKYGN ANVWKYFTDL FDYLPLTALV D GQIFCLHG ...String:
MDEKVFTKEL DQWIEQLNEC KQLSESQVKS LCEKAKEILT KESNVQEVRC PVTVCGDVHG QFHDLMELFR IGGKSPDTNY LFMGDYVNR GYYSVETVTL LVALKVRYRE RITILRGNHE SRQITQVYGF YDECLRKYGN ANVWKYFTDL FDYLPLTALV D GQIFCLHG GLSPSIDTLD HIRALDRLQE VPHEGPMCDL LWSDPDDRGG WGISPRGAGY TFGQDISETF NHANGLTLVS RA HQLVMEG YNWCHDRNVV TIFSAPNYCY RCGNQAAIME LDDTLKYSFL QFDPAPRRGE PHVTRRTPDY FL

UniProtKB: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform

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Macromolecule #4: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MN
Molecular weightTheoretical: 54.938 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 242161
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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