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

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Basic information

Entry
Database: PDB / ID: 6fud
TitleComplex of rice blast (Magnaporthe oryzae) effector protein AVR-PikA with the HMA domain of Pikm-1 from rice (Oryza sativa)
Components
  • AVR-Pik protein
  • NBS-LRR class disease resistance protein
KeywordsANTIFUNGAL PROTEIN / Plant NLR / fungal effector / Plant immunity / Complex
Function / homology
Function and homology information


response to other organism / defense response / ADP binding / ATP binding / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Disease resistance protein Pikm1-TS / AVR-Pik protein
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
Magnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsFranceschetti, M. / De la Concepcion, J.C. / Banfield, M.J.
Funding support United Kingdom, Japan, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J00453 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P012574 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M02198X United Kingdom
European Research Council743165
Japan Society for the Promotion of ScienceKAKENHI 15H05779 Japan
CitationJournal: Nat Plants / Year: 2018
Title: Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen.
Authors: De la Concepcion, J.C. / Franceschetti, M. / Maqbool, A. / Saitoh, H. / Terauchi, R. / Kamoun, S. / Banfield, M.J.
History
DepositionFeb 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 15, 2018Group: 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_author.identifier_ORCID
Revision 1.3Jan 17, 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
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: NBS-LRR class disease resistance protein
B: AVR-Pik protein


Theoretical massNumber of molelcules
Total (without water)19,3832
Polymers19,3832
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-6 kcal/mol
Surface area8310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.070, 54.440, 46.640
Angle α, β, γ (deg.)90.00, 104.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NBS-LRR class disease resistance protein


Mass: 8547.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: Pikm1-TS, Pi-km1 / Production host: Escherichia coli (E. coli) / References: UniProt: B5UBC1
#2: Protein AVR-Pik protein / AVR-Pikm protein


Mass: 10835.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Gene: AVR-Pik, AVR-Pikm / Production host: Escherichia coli (E. coli) / References: UniProt: C4B8B9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 1.91 Å3/Da / Density % sol: 35.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.12M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol); 0.1M Buffer system 2 (1M sodium HEPES, MOPS (acid)) pH ...Details: 0.12M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol); 0.1M Buffer system 2 (1M sodium HEPES, MOPS (acid)) pH 7.5; 50% v/v Precipitant mix 4 (25%v/v MPD; 25%v/v PEG 1000; 25%v/v PEG3350)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→34.76 Å / Num. obs: 33854 / % possible obs: 99.3 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 21.5
Reflection shellResolution: 1.3→1.33 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia20.4.0.0data reduction
Aimless0.5.17data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A6W

5a6w


Resolution: 1.3→34.76 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.471 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.044 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16191 1720 4.8 %RANDOM
Rwork0.12542 ---
obs0.12719 33854 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.458 Å2
Baniso -1Baniso -2Baniso -3
1--1.68 Å20 Å20.67 Å2
2---0.06 Å20 Å2
3---1.24 Å2
Refinement stepCycle: 1 / Resolution: 1.3→34.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1239 0 0 144 1383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191330
X-RAY DIFFRACTIONr_bond_other_d0.0020.021268
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.9571812
X-RAY DIFFRACTIONr_angle_other_deg0.98432961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9685175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26924.33360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1215243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.647159
X-RAY DIFFRACTIONr_chiral_restr0.1150.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211484
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02269
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_it2.7591.953650
X-RAY DIFFRACTIONr_mcbond_other2.7421.949649
X-RAY DIFFRACTIONr_mcangle_it3.5222.94813
X-RAY DIFFRACTIONr_mcangle_other3.522.942814
X-RAY DIFFRACTIONr_scbond_it3.9962.265680
X-RAY DIFFRACTIONr_scbond_other3.9912.264680
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9943.268989
X-RAY DIFFRACTIONr_long_range_B_refined5.66724.5481458
X-RAY DIFFRACTIONr_long_range_B_other5.66524.5481459
X-RAY DIFFRACTIONr_rigid_bond_restr2.8332598
X-RAY DIFFRACTIONr_sphericity_free33.372588
X-RAY DIFFRACTIONr_sphericity_bonded14.30452616
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 123 -
Rwork0.171 2277 -
obs--91.6 %

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