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- PDB-8b2r: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -

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Basic information

Entry
Database: PDB / ID: 8b2r
TitleComplex of rice blast (Magnaporthe oryzae) effector protein AVR-PikF with a rice (Oryza sativa) RGA5 HMA domain mutant.
Components
  • AVR-Pik protein
  • Disease resistance protein RGA5
KeywordsANTIFUNGAL PROTEIN / heavy-metal associated domain / plant immunity / fungal pathogen / Magnaporthe oryzae / rice blast / rice / NLR / MAX effector
Function / homology
Function and homology information


plant-type hypersensitive response / innate immune response-activating signaling pathway / ADP binding / : / defense response to bacterium / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
AVR-Pik protein / Disease resistance protein RGA5
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
Pyricularia oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsBentham, A.R. / Banfield, M.J.
Funding support United Kingdom, European Union, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012574 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/J/000PR9797 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011216/1 United Kingdom
European Research Council (ERC)743165European Union
John Innes Foundation United Kingdom
CitationJournal: Plant Cell / Year: 2023
Title: Allelic compatibility in plant immune receptors facilitates engineering of new effector recognition specificities.
Authors: Bentham, A.R. / De la Concepcion, J.C. / Benjumea, J.V. / Kourelis, J. / Jones, S. / Mendel, M. / Stubbs, J. / Stevenson, C.E.M. / Maidment, J.H.R. / Youles, M. / Zdrzalek, R. / Kamoun, S. / Banfield, M.J.
History
DepositionSep 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 2, 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Disease resistance protein RGA5
B: AVR-Pik protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5616
Polymers18,3322
Non-polymers2294
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, surface plasmon resonance, immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-19 kcal/mol
Surface area8850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.906, 57.896, 76.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Disease resistance protein RGA5 / Os11gRGA5 / SasRGA5


Mass: 8409.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: RGA5 / Production host: Escherichia coli (E. coli) / References: UniProt: F7J0N2
#2: Protein AVR-Pik protein / AVR-Pik protein ( Pikmprotein / Pikp protein ) / AvrPi7 protein


Mass: 9922.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyricularia oryzae (rice blast fungus) / Gene: AVR-Pik, AvrPik, Pikm, Pikp / Production host: Escherichia coli (E. coli) / References: UniProt: C4B8B8

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Non-polymers , 4 types, 184 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.93 Å3/Da / Density % sol: 36.3 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M BIS-TRIS pH 5.5 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.22→46.242 Å / Num. obs: 42985 / % possible obs: 99.4 % / Redundancy: 11.5 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.5
Reflection shellResolution: 1.22→1.24 Å / Rmerge(I) obs: 1.719 / Num. unique obs: 1915 / CC1/2: 0.324

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B1I

7b1i


Resolution: 1.22→46.242 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.192 / WRfactor Rwork: 0.141 / SU B: 2.294 / SU ML: 0.043 / Average fsc free: 0.958 / Average fsc work: 0.9747 / Cross valid method: FREE R-VALUE / ESU R: 0.044 / ESU R Free: 0.049
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2037 2125 4.961 %
Rwork0.1502 40711 -
all0.153 --
obs-42836 99.397 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.484 Å2
Baniso -1Baniso -2Baniso -3
1--1.955 Å20 Å2-0 Å2
2--0.582 Å20 Å2
3---1.373 Å2
Refinement stepCycle: LAST / Resolution: 1.22→46.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 11 180 1473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121364
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161277
X-RAY DIFFRACTIONr_angle_refined_deg1.8081.6441846
X-RAY DIFFRACTIONr_angle_other_deg0.6141.5752992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7285173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.678512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67710247
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.161061
X-RAY DIFFRACTIONr_chiral_restr0.1010.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021570
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02262
X-RAY DIFFRACTIONr_nbd_refined0.2860.2200
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.21174
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2646
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.2743
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2890.2104
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.210.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2750.216
X-RAY DIFFRACTIONr_nbd_other0.2360.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3280.231
X-RAY DIFFRACTIONr_mcbond_it2.2071.108675
X-RAY DIFFRACTIONr_mcbond_other2.2071.107675
X-RAY DIFFRACTIONr_mcangle_it2.6441.669846
X-RAY DIFFRACTIONr_mcangle_other2.6421.67847
X-RAY DIFFRACTIONr_scbond_it3.5751.396689
X-RAY DIFFRACTIONr_scbond_other3.5731.395690
X-RAY DIFFRACTIONr_scangle_it3.9841.995997
X-RAY DIFFRACTIONr_scangle_other3.9821.995998
X-RAY DIFFRACTIONr_lrange_it4.21824.7971509
X-RAY DIFFRACTIONr_lrange_other4.12923.2231481
X-RAY DIFFRACTIONr_rigid_bond_restr5.43732641
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.22-1.2520.3451460.31427810.31631340.8830.91393.3950.316
1.252-1.2860.3041660.2828510.28130670.9270.93598.36970.28
1.286-1.3230.2591530.24328160.24429700.9440.95199.96630.239
1.323-1.3640.3031480.21427380.21828860.9320.9671000.205
1.364-1.4090.2661430.18126720.18528150.9530.9771000.168
1.409-1.4580.2181290.16526090.16827380.9650.9811000.15
1.458-1.5130.2311370.15524780.15926160.9590.98599.96180.136
1.513-1.5750.1811280.12824080.13125360.9820.991000.111
1.575-1.6450.1831160.11722850.1224020.9790.99199.95840.1
1.645-1.7250.2041030.11522420.11823450.9740.9911000.097
1.725-1.8180.1651000.12221230.12422230.9830.9911000.106
1.818-1.9280.2061090.12520070.1321160.9740.991000.111
1.928-2.0610.1771030.1218880.12319910.9810.9911000.109
2.061-2.2260.187860.12417650.12618510.980.9911000.114
2.226-2.4380.163790.13516530.13617320.9830.9891000.127
2.438-2.7240.199690.13714850.1415540.9750.9881000.133
2.724-3.1440.18700.14713260.14813960.9760.9861000.145
3.144-3.8460.215700.14811330.15112030.9690.9861000.152
3.846-5.4210.204480.1449010.1469490.9810.9891000.157
5.421-46.2420.186220.215500.2085720.9610.9691000.219
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)
11.15810.2991-0.13511.9644-0.48531.4056-0.0190.11880.0291-0.1265-0.0121-0.0595-0.04350.05120.03110.0442-0.002-0.00030.01740.0050.003712.3203-1.0959-16.6194
21.5849-0.1306-0.33771.29440.68361.65640.0137-0.12230.12490.01510.01780.0257-0.10720.0135-0.03150.0249-0.00440.00260.0121-0.00820.01172.1982-0.3647-0.307
Refinement TLS groupSelection: ALL

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