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- PDB-7xvk: Modularity of Phytophthora effectors enables host mimicry of a pr... -

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Basic information

Entry
Database: PDB / ID: 7xvk
TitleModularity of Phytophthora effectors enables host mimicry of a principal phosphatase
Components
  • RxLR effector protein PSR2
  • Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform
KeywordsIMMUNE SYSTEM / plant immunology / translocation / effector / phosphatase
Function / homology
Function and homology information


regulation of phosphorylation / peroxisome / host cell / extracellular region / nucleus / cytosol
Similarity search - Function
: / Effector PexRD54, WY-domain / : / HEAT repeat / HEAT repeat / PPP2R1A-like HEAT repeat / HEAT repeat profile. / HEAT, type 2 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant ...: / Effector PexRD54, WY-domain / : / HEAT repeat / HEAT repeat / PPP2R1A-like HEAT repeat / HEAT repeat profile. / HEAT, type 2 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
RxLR effector protein PSR2 / Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Phytophthora sojae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsWang, J. / Wang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930065 China
National Natural Science Foundation of China (NSFC)31725008 China
CitationJournal: Cell / Year: 2023
Title: Pathogen protein modularity enables elaborate mimicry of a host phosphatase.
Authors: Li, H. / Wang, J. / Kuan, T.A. / Tang, B. / Feng, L. / Wang, J. / Cheng, Z. / Sklenar, J. / Derbyshire, P. / Hulin, M. / Li, Y. / Zhai, Y. / Hou, Y. / Menke, F.L.H. / Wang, Y. / Ma, W.
History
DepositionMay 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 2, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform
B: RxLR effector protein PSR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,0544
Polymers111,9292
Non-polymers1242
Water14,970831
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.211, 111.552, 161.756
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform / AtA beta / PP2A / subunit A / beta isoform


Mass: 43547.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PP2AA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38950
#2: Protein RxLR effector protein PSR2 / Avirulence homolog protein 146 / Suppressor of RNA silencing protein 2


Mass: 68382.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora sojae (eukaryote) / Gene: PSR2 / Production host: Escherichia coli (E. coli) / References: UniProt: E0W4V5
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 831 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 5% PEG 20000 0.1 M Bis tris pH 5.8 5 mM MgSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 62511 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.027 / Rrim(I) all: 0.068 / Χ2: 0.932 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.386.50.6461420.8330.270.6960.92299.6
2.38-2.486.30.45861260.9080.1950.4990.92699.7
2.48-2.5960.32661870.9420.1440.3570.99899.8
2.59-2.736.50.2661880.9680.1090.2831.00399.9
2.73-2.96.60.17662150.9830.0740.1920.942100
2.9-3.126.30.11861860.9910.0510.1291.00399.9
3.12-3.446.60.07562530.9960.0320.0820.986100
3.44-3.936.60.04762740.9980.020.0510.994100
3.93-4.956.50.03163430.9980.0130.0330.878100
4.95-506.20.02465970.9990.0110.0270.67499.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GNC,2NPP

5gnc

2npp


Resolution: 2.29→38.77 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2267 2000 3.23 %
Rwork0.2088 59929 -
obs0.2093 61929 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.07 Å2 / Biso mean: 39.5009 Å2 / Biso min: 5.85 Å2
Refinement stepCycle: final / Resolution: 2.29→38.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7734 0 20 831 8585
Biso mean--76.85 41.49 -
Num. residues----990
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.29-2.350.34991270.27753820394790
2.35-2.410.28811390.27134158429797
2.41-2.480.26721410.25764238437999
2.48-2.560.30211410.244442314372100
2.56-2.660.27881440.238743044448100
2.66-2.760.25091420.238242704412100
2.76-2.890.26021440.230743014445100
2.89-3.040.27621440.23442944438100
3.04-3.230.25531430.228543064449100
3.23-3.480.23981450.205143264471100
3.48-3.830.20531450.189743524497100
3.83-4.380.1951450.175143584503100
4.38-5.520.15891460.175344034549100
5.52-38.770.17571540.183145684722100

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