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- PDB-8r7a: Complex of rice blast (Magnaporthe oryzae) effector protein PWL2 ... -

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Basic information

Entry
Database: PDB / ID: 8r7a
TitleComplex of rice blast (Magnaporthe oryzae) effector protein PWL2 with the HMA domain of OsHIPP43 from rice (Oryza sativa)
Components
  • Os01g0507700 protein
  • Pwl2 protein
KeywordsPLANT PROTEIN / Pathogen effector / host target protein / rice blast / disease resistance
Function / homologyHeavy metal binding protein HIPP/ATX1-like / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / metal ion binding / Pwl2 protein / Os01g0507700 protein
Function and homology information
Biological speciesOryza sativa (Asian cultivated rice)
Pyricularia oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsZdrzalek, R. / Banfield, M.J.
Funding support United Kingdom, European Union, Japan, 14items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W00108X/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/WW002221/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V002937/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V016342 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V015508/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012574 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/J/000PR9795 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/J/000PR9796 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X010996/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011216/1 United Kingdom
European Research Council (ERC)743165European Union
Japan Society for the Promotion of Science (JSPS)20H05681 Japan
Gatsby Charitable Foundation United Kingdom
John Innes Foundation United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Bioengineering a plant NLR immune receptor with a robust binding interface toward a conserved fungal pathogen effector.
Authors: Zdrzalek, R. / Xi, Y. / Langner, T. / Bentham, A.R. / Petit-Houdenot, Y. / De la Concepcion, J.C. / Harant, A. / Shimizu, M. / Were, V. / Talbot, N.J. / Terauchi, R. / Kamoun, S. / Banfield, M.J.
History
DepositionNov 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Os01g0507700 protein
B: Pwl2 protein


Theoretical massNumber of molelcules
Total (without water)32,8562
Polymers32,8562
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-8 kcal/mol
Surface area9030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.161, 63.161, 198.208
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-242-

HOH

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Components

#1: Protein Os01g0507700 protein


Mass: 16658.377 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: Os01g0507700 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LJL3
#2: Protein Pwl2 protein


Mass: 16197.554 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyricularia oryzae (rice blast fungus) / Gene: MGG_04301 / Production host: Escherichia coli (E. coli) / References: UniProt: G5EI71
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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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 % sol: 29.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Tris 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→54.76 Å / Num. obs: 22749 / % possible obs: 100 % / Redundancy: 36.9 % / CC1/2: 1 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.014 / Rrim(I) all: 0.087 / Χ2: 0.94 / Net I/σ(I): 31.1
Reflection shellResolution: 1.8→1.84 Å / % possible obs: 100 % / Redundancy: 38.4 % / Rmerge(I) obs: 1.676 / Num. measured all: 49513 / Num. unique obs: 1291 / CC1/2: 0.915 / Rpim(I) all: 0.271 / Rrim(I) all: 1.698 / Χ2: 0.87 / Net I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
xia2data reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→54.76 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.05 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2151 1134 5 %RANDOM
Rwork0.18835 ---
obs0.1897 21509 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.789 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.15 Å20 Å2
2--0.31 Å2-0 Å2
3----1 Å2
Refinement stepCycle: 1 / Resolution: 1.8→54.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1465 0 0 175 1640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121515
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161347
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.8532044
X-RAY DIFFRACTIONr_angle_other_deg0.5711.7953114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5145187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.786514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7810243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02376
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6771.89748
X-RAY DIFFRACTIONr_mcbond_other1.6731.89748
X-RAY DIFFRACTIONr_mcangle_it2.4693.377932
X-RAY DIFFRACTIONr_mcangle_other2.4683.381933
X-RAY DIFFRACTIONr_scbond_it2.4512.195767
X-RAY DIFFRACTIONr_scbond_other2.452.199768
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8143.8871112
X-RAY DIFFRACTIONr_long_range_B_refined7.89820.441751
X-RAY DIFFRACTIONr_long_range_B_other7.8419.511705
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 75 -
Rwork0.251 1524 -
obs--99.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.8458-2.32421.26394.3307-0.16086.94230.45420.1230.3735-0.4276-0.4088-0.2658-0.40210.3067-0.04550.14490.04140.06660.0760.02220.038717.423.21112.652
24.1523-2.11780.0542.6522-0.54435.57830.42010.16890.0279-0.6613-0.21890.3021-0.1048-0.3458-0.20120.21020.0902-0.07310.0563-0.0130.06877.15623.89810.44
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 100
2X-RAY DIFFRACTION2B23 - 134

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