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

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Basic information

Entry
Database: PDB / ID: 7qzd
TitleComplex of rice blast (Magnaporthe oryzae) effector protein AVR-PikF with an engineered HMA domain of Pikp-1 (Pikp-SNK-EKE) from rice (Oryza sativa)
Components
  • Avr-Pik
  • 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
Avr-Pik / Resistance protein Pikp-1
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
Pyricularia oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMaidment, J.H.R. / Franceschetti, M. / Longya, A. / 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 31, 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 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Resistance protein Pikp-1
B: Resistance protein Pikp-1
C: Avr-Pik
E: Resistance protein Pikp-1
F: Resistance protein Pikp-1
G: Avr-Pik


Theoretical massNumber of molelcules
Total (without water)55,3906
Polymers55,3906
Non-polymers00
Water1,964109
1
A: Resistance protein Pikp-1
B: Resistance protein Pikp-1
C: Avr-Pik


Theoretical massNumber of molelcules
Total (without water)27,6953
Polymers27,6953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-5 kcal/mol
Surface area11610 Å2
2
E: Resistance protein Pikp-1
F: Resistance protein Pikp-1
G: Avr-Pik


Theoretical massNumber of molelcules
Total (without water)27,6953
Polymers27,6953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-6 kcal/mol
Surface area11380 Å2
Unit cell
Length a, b, c (Å)67.381, 80.782, 103.804
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 / Avr-Pik protein


Mass: 10833.278 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) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A219T3Y8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.5 Å3/Da / Density % sol: 50.77 %
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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→103.8 Å / Num. obs: 28553 / % possible obs: 97.4 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.038 / Rrim(I) all: 0.105 / Net I/σ(I): 11.5 / Num. measured all: 195704 / Scaling rejects: 28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.276.70.7511687025120.8440.3020.8142.299
9.07-103.860.03527454570.9990.0150.03932.593.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A6W

5a6w


Resolution: 2.2→63.83 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.2758 / WRfactor Rwork: 0.2169 / FOM work R set: 0.731 / SU B: 17.721 / SU ML: 0.214 / SU R Cruickshank DPI: 0.2819 / SU Rfree: 0.2367 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.282 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2855 1437 5 %RANDOM
Rwork0.2313 ---
obs0.234 27072 96.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.56 Å2 / Biso mean: 42.021 Å2 / Biso min: 19.77 Å2
Baniso -1Baniso -2Baniso -3
1--2.79 Å20 Å2-0 Å2
2--3.51 Å20 Å2
3----0.72 Å2
Refinement stepCycle: final / Resolution: 2.2→63.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3526 0 0 109 3635
Biso mean---36.71 -
Num. residues----458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133575
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163608
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.634807
X-RAY DIFFRACTIONr_angle_other_deg1.1921.68321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1765449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69323.373166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.38815680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8461520
X-RAY DIFFRACTIONr_chiral_restr0.0630.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023969
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02747
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 115 -
Rwork0.363 2013 -
all-2128 -
obs--98.61 %
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)
16.1495-1.2535-2.00195.2342-1.67315.77120.052-0.02450.6615-0.0962-0.006-0.4332-0.49410.4071-0.0460.1142-0.03860.0470.08070.010.2531-5.136311.7525-7.9365
23.40331.70030.06244.44130.76824.29340.0126-0.17990.3344-0.03880.19230.4207-0.4187-0.4626-0.20490.0640.03810.03620.10410.01770.1107-20.51346.26511.5914
35.29060.56860.51972.53540.06322.04150.1554-0.0899-0.1282-0.1132-0.1064-0.11410.1938-0.0328-0.0490.03150.01080.00020.03250.01160.0088-25.965-10.3748-2.3826
43.89512.57321.29475.0828-1.50116.81220.26110.1102-0.35660.1424-0.0158-0.52540.55050.2757-0.24530.10510.0186-0.08760.14730.00790.2171-38.2956-12.839124.2548
53.7566-1.50991.05134.04232.13292.91550.0617-0.1339-0.25320.24950.03920.26330.1257-0.2512-0.10090.03720.00850.03250.20760.01410.0651-54.1909-7.96814.6831
64.831-0.33830.39631.5725-0.3953.40080.0228-0.20870.420.1665-0.03760.0132-0.3893-0.02830.01480.11060.00790.02160.0519-0.03690.0522-59.67798.76318.3762
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A187 - 259
2X-RAY DIFFRACTION2B187 - 263
3X-RAY DIFFRACTION3C32 - 113
4X-RAY DIFFRACTION4E188 - 259
5X-RAY DIFFRACTION5F187 - 262
6X-RAY DIFFRACTION6G32 - 113

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