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- PDB-6q76: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -

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Basic information

Entry
Database: PDB / ID: 6q76
TitleComplex of rice blast (Magnaporthe oryzae) effector protein AVR-Pia with the HMA domain of Pikp-1 from rice (Oryza sativa)
Components
  • AVR-Pia protein
  • Resistance protein Pikp-1
KeywordsANTIFUNGAL PROTEIN / Effector / Heavy metal-associated / NLR / MAX
Function / homology
Function and homology information


defense response to other organism / ADP binding / ATP hydrolysis activity / metal ion binding
Similarity search - Function
Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat domain superfamily / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
AVR-Pia protein / Resistance protein Pikp-1
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
Magnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVarden, F.A. / Banfield, M.J.
Funding support2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council
European Research Council
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Cross-reactivity of a rice NLR immune receptor to distinct effectors from the rice blast pathogenMagnaporthe oryzaeprovides partial disease resistance.
Authors: Varden, F.A. / Saitoh, H. / Yoshino, K. / Franceschetti, M. / Kamoun, S. / Terauchi, R. / Banfield, M.J.
History
DepositionDec 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Resistance protein Pikp-1
B: AVR-Pia protein


Theoretical massNumber of molelcules
Total (without water)15,4072
Polymers15,4072
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-5 kcal/mol
Surface area7930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.844, 53.444, 117.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Resistance protein Pikp-1


Mass: 7861.272 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: Pikp-1 / Production host: Escherichia coli (E. coli) / References: UniProt: E9KPB5
#2: Protein AVR-Pia protein


Mass: 7545.610 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Gene: AVR-Pia / Production host: Escherichia coli (E. coli) / References: UniProt: B9WZW9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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 Matthews: 3.56 Å3/Da / Density % sol: 65.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.12 M Alcohols (0.2 M 1,6-Hexanediol; 0.2 M 1-Butanol; 0.2 M 1,2-Propanediol; 0.2 M 2-Propanol; 0.2 M 1,4-Butanediol; 0.2 M 1,3-Propanediol), 0.1 M Buffer System 1 (1.0 M imidazole; MES ...Details: 0.12 M Alcohols (0.2 M 1,6-Hexanediol; 0.2 M 1-Butanol; 0.2 M 1,2-Propanediol; 0.2 M 2-Propanol; 0.2 M 1,4-Butanediol; 0.2 M 1,3-Propanediol), 0.1 M Buffer System 1 (1.0 M imidazole; MES monohydrate (acid), pH 6.5) and 50 % v/v Precipitant Mix 2 (40 % v/v Ethylene glycol; 20 % w/v PEG 8000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→48.72 Å / Num. obs: 18107 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.057 / Net I/σ(I): 19.7
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 13.3 % / Num. unique obs: 1151 / CC1/2: 0.81 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
xia20.5.328data reduction
Aimless0.7.3data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MYW, 5A6P

2myw

5a6p


Resolution: 1.9→48.72 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.986 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.123
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 962 5.3 %RANDOM
Rwork0.2031 ---
obs0.2053 17101 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 126.51 Å2 / Biso mean: 52.819 Å2 / Biso min: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.52 Å20 Å20 Å2
2---2.04 Å20 Å2
3----2.48 Å2
Refinement stepCycle: final / Resolution: 1.9→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1066 0 0 89 1155
Biso mean---58.06 -
Num. residues----141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0141081
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171047
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.6541461
X-RAY DIFFRACTIONr_angle_other_deg0.941.6422442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.11321.91547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28515193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.84157
X-RAY DIFFRACTIONr_chiral_restr0.0750.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021193
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02179
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 72 -
Rwork0.358 1237 -
all-1309 -
obs--99.92 %

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