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- PDB-6r8k: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -

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Basic information

Entry
Database: PDB / ID: 6r8k
TitleComplex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with an engineered HMA domain of Pikp-1 from rice (Oryza sativa)
Components
  • AVR-Pik protein
  • NBS-LRR class disease resistance protein Pikh-1
KeywordsPLANT PROTEIN / NLR / Complex / HMA / Rice blast
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 / 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-Pik protein / NBS-LRR class disease resistance protein
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
Magnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDe la Concepcion, J.C. / Franceschetti, M. / Banfield, M.J.
Funding support United Kingdom, Japan, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J004553 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P012574 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M02198X United Kingdom
European Research Council743165 United Kingdom
Japan Society for the Promotion of ScienceKAKENHI 15H05779 Japan
Citation
Journal: Elife / Year: 2019
Title: Protein engineering expands the effector recognition profile of a rice NLR immune receptor.
Authors: De la Concepcion, J.C. / Franceschetti, M. / MacLean, D. / Terauchi, R. / Kamoun, S. / Banfield, M.J.
#1: Journal: Biorxiv / Year: 2019
Title: Protein engineering expands the effector recognition profile of a rice NLR immune receptor
Authors: De la Concepcion, J.C. / Franceschetti, M. / Terauchi, R. / Kamoun, S. / Banfield, M.J.
History
DepositionApr 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Sep 18, 2019Group: Data collection / Experimental preparation / Refinement description
Category: exptl_crystal_grow / software / Item: _exptl_crystal_grow.pdbx_details / _software.version
Revision 1.3Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.4Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 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
B: NBS-LRR class disease resistance protein Pikh-1
C: AVR-Pik protein


Theoretical massNumber of molelcules
Total (without water)19,2162
Polymers19,2162
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-4 kcal/mol
Surface area8430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.790, 65.330, 75.860
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 NBS-LRR class disease resistance protein Pikh-1


Mass: 8388.819 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: Pi-km1, Pikh-1 / Production host: Escherichia coli (E. coli) / References: UniProt: D5L9G5
#2: Protein AVR-Pik protein / AVR-Pik protein ( Pikmprotein / Pikp protein ) / AvrPi7 protein


Mass: 10827.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Gene: AVR-Pik, AvrPik, Pikm, Pikp / Production host: Escherichia coli (E. coli) / References: UniProt: C4B8B8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 1.92 Å3/Da / Density % sol: 36.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
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 1 (1M Imidazole, MES monohydrate ...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 1 (1M Imidazole, MES monohydrate (acid)) pH 6.5, 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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→32.8 Å / Num. obs: 20294 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.024 / Rrim(I) all: 0.084 / Net I/σ(I): 16.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.971 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 978 / CC1/2: 0.866 / Rpim(I) all: 0.38 / Rrim(I) all: 1.01 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G10

6g10


Resolution: 1.6→32.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.987 / SU ML: 0.07 / SU R Cruickshank DPI: 0.1029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.102
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1001 4.9 %RANDOM
Rwork0.1966 ---
obs0.1983 19242 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.56 Å2 / Biso mean: 25.609 Å2 / Biso min: 13.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.86 Å2
Refinement stepCycle: final / Resolution: 1.6→32.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1248 0 0 126 1374
Biso mean---32.4 -
Num. residues----160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131307
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171250
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.6361768
X-RAY DIFFRACTIONr_angle_other_deg1.3391.5942908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8015166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.97722.27366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.46715236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.226159
X-RAY DIFFRACTIONr_chiral_restr0.0630.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021469
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02270
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 76 -
Rwork0.255 1401 -
all-1477 -
obs--100 %

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