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- PDB-7qpx: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -

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Basic information

Entry
Database: PDB / ID: 7qpx
TitleComplex of rice blast (Magnaporthe oryzae) effector protein AVR-PikC with an engineered HMA domain of Pikp-1 (Pikp-SNK-EKE) from rice (Oryza sativa)
Components
  • AVR-Pik protein
  • Resistance protein Pikp-1
KeywordsANTIFUNGAL PROTEIN / Plant immunity / pathogen effector / protein engineering / blast disease
Function / homology
Function and homology information


defense response to other organism / ADP binding / ATP hydrolysis activity / metal ion binding
Similarity search - Function
: / AVR-Pik-like, HMA interaction domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein Winged helix domain / Disease resistance protein, plants / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA ...: / AVR-Pik-like, HMA interaction domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein Winged helix domain / Disease resistance protein, plants / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / : / Leucine-rich repeat region / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat domain superfamily / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Resistance protein Pikp-1 / AVR-Pik-like HMA interaction domain-containing protein
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
Pyricularia oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMaidment, J.H.R. / Banfield, M.J.
Funding support Japan, 9items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011216/1 Japan
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012574 Japan
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/J/000PR9795 Japan
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M02198X Japan
European Research Council (ERC)743165 Japan
The Thailand Research Fund (TRF)PHD/0152/2556 Japan
John Innes Foundation Japan
Japan Society for the Promotion of Science (JSPS)KAKENHI 15H05779 Japan
Japan Society for the Promotion of Science (JSPS)KAKENHI 20H00421 Japan
Citation
Journal: Elife / Year: 2023
Title: Effector target-guided engineering of an integrated domain expands the disease resistance profile of a rice NLR immune receptor.
Authors: Maidment, J.H.R. / Shimizu, M. / Bentham, A.R. / Vera, S. / Franceschetti, M. / Longya, A. / Stevenson, C.E.M. / De la Concepcion, J.C. / Bialas, A. / Kamoun, S. / Terauchi, R. / Banfield, M.J.
#1: Journal: Biorxiv / Year: 2022
Title: Effector target-guided engineering of an integrated domain expands the disease resistance profile of a rice NLR immune receptor
Authors: Maidment, J. / Shimizu, M. / Vera, S. / Franceschetti, M. / Longya, A. / Stevenson, C. / De la Concepcion, J. / Bialas, A. / Kamoun, S. / Terauchi, R. / Banfield, M.
History
DepositionJan 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 31, 2023Group: Database references / Category: citation / citation_author
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Resistance protein Pikp-1
B: Resistance protein Pikp-1
C: AVR-Pik protein
D: Resistance protein Pikp-1
E: Resistance protein Pikp-1
F: AVR-Pik protein


Theoretical massNumber of molelcules
Total (without water)55,4186
Polymers55,4186
Non-polymers00
Water3,657203
1
A: Resistance protein Pikp-1
B: Resistance protein Pikp-1
C: AVR-Pik protein


Theoretical massNumber of molelcules
Total (without water)27,7093
Polymers27,7093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-9 kcal/mol
Surface area11310 Å2
MethodPISA
2
D: Resistance protein Pikp-1
E: Resistance protein Pikp-1
F: AVR-Pik protein


Theoretical massNumber of molelcules
Total (without water)27,7093
Polymers27,7093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-9 kcal/mol
Surface area11020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.353, 83.130, 107.035
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Resistance protein Pikp-1


Mass: 8430.855 Da / Num. of mol.: 4 / Mutation: S258E, N261K, K262E
Source method: isolated from a genetically manipulated source
Details: expressed protein corresponds to residues 186-263 of wild type sequence. N-terminal GP is a scar from the cleaved expression tag
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: Pikp-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9KPB5
#2: Protein AVR-Pik protein


Mass: 10847.306 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: expressed protein corresponds to residues 22-113 of wild type sequence. N-terminal M was added.
Source: (gene. exp.) Pyricularia oryzae (rice blast fungus) / Strain: 70-15 / ATCC MYA-4617 / FGSC 8958 / Gene: MGG_15972 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G4MXW3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: NULL

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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: Feb 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.05→46.71 Å / Num. obs: 37795 / % possible obs: 99.8 % / Redundancy: 9.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.027 / Rrim(I) all: 0.085 / Net I/σ(I): 15.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.05-2.1110.11.04828860.8380.341.10399.4
8.94-46.7180.0385340.9980.0140.04199.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimless0.6.1data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7A8W

7a8w


Resolution: 2.05→46.71 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.2199 / WRfactor Rwork: 0.2012 / FOM work R set: 0.8268 / SU B: 4.484 / SU ML: 0.117 / SU R Cruickshank DPI: 0.1789 / SU Rfree: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 1898 5 %RANDOM
Rwork0.2044 ---
obs0.2056 35848 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.01 Å2 / Biso mean: 43.89 Å2 / Biso min: 26.78 Å2
Baniso -1Baniso -2Baniso -3
1--2.41 Å20 Å2-0 Å2
2--1.68 Å20 Å2
3---0.72 Å2
Refinement stepCycle: final / Resolution: 2.05→46.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 0 203 3661
Biso mean---46.48 -
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133550
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163603
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.634783
X-RAY DIFFRACTIONr_angle_other_deg1.231.5998318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2615452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.52722.963162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.10815677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2161521
X-RAY DIFFRACTIONr_chiral_restr0.0620.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023930
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02740
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 151 -
Rwork0.277 2584 -
all-2735 -
obs--98.99 %

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