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- PDB-7pp2: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -

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Basic information

Entry
Database: PDB / ID: 7pp2
TitleComplex of rice blast (Magnaporthe oryzae) effector protein AVR-Pii with the host target Exo70F2 from Rice (Oryza sativa)
Components
  • AVR-Pii protein
  • Exocyst subunit Exo70 family protein
KeywordsPLANT PROTEIN / Complex / Zinc-finger fold / Exocyst / plant-pathogen interactions
Function / homologyExocyst complex subunit Exo70, C-terminal / Exocyst complex component Exo70 / Exo70 exocyst complex subunit C-terminal / exocyst / Cullin repeat-like-containing domain superfamily / exocytosis / protein transport / Exocyst subunit Exo70 family protein / AVR-Pii protein
Function and homology information
Biological speciesOryza sativa (Asian cultivated rice)
Pyricularia oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.69 Å
AuthorsDe la Concepcion, J.C. / Bentham, A.R. / Lawson, D. / Banfield, M.J.
Funding support United Kingdom, 3items
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
John Innes Foundation United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: A blast fungus zinc-finger fold effector binds to a hydrophobic pocket in host Exo70 proteins to modulate immune recognition in rice.
Authors: De la Concepcion, J.C. / Fujisaki, K. / Bentham, A.R. / Cruz Mireles, N. / Sanchez de Medina Hernandez, V. / Shimizu, M. / Lawson, D.M. / Kamoun, S. / Terauchi, R. / Banfield, M.J.
History
DepositionSep 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 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_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exocyst subunit Exo70 family protein
B: AVR-Pii protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9173
Polymers72,8522
Non-polymers651
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-15 kcal/mol
Surface area24440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.316, 76.621, 67.873
Angle α, β, γ (deg.)90.000, 107.760, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Exocyst subunit Exo70 family protein


Mass: 67318.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: OJ1003_F04.39-1, Os02g0505400, OsJ_06848 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N7KFC4
#2: Protein AVR-Pii protein


Mass: 5532.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyricularia oryzae (rice blast fungus) / Gene: AVR-Pii, Avr-Pii / Production host: Escherichia coli (E. coli) / References: UniProt: C4B8B7
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.3 M Ammonium iodide; 30% 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: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.69→66.81 Å / Num. obs: 19153 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rrim(I) all: 0.156 / Net I/σ(I): 8.4
Reflection shellResolution: 2.69→2.82 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2534 / CC1/2: 0.541 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RL5

4rl5


Resolution: 2.69→66.56 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.913 / SU B: 38.498 / SU ML: 0.338 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.745 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2792 975 5.1 %RANDOM
Rwork0.2516 ---
obs0.253 18163 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 173.44 Å2 / Biso mean: 80.885 Å2 / Biso min: 51.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å2-0 Å22.99 Å2
2---8.55 Å20 Å2
3---5.3 Å2
Refinement stepCycle: final / Resolution: 2.69→66.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3738 0 1 1 3740
Biso mean--62.02 52.47 -
Num. residues----469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133798
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173665
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.6385119
X-RAY DIFFRACTIONr_angle_other_deg1.0671.5848433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6295460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11721.848211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59815693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.021531
X-RAY DIFFRACTIONr_chiral_restr0.0430.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024225
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02861
LS refinement shellResolution: 2.69→2.76 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 77 -
Rwork0.341 1320 -
all-1397 -
obs--99.29 %
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)
10.9422-1.0317-0.15653.39740.7771.1752-0.07090.1171-0.13190.0381-0.04210.14960.1916-0.01460.1130.0643-0.04010.05380.3079-0.00590.0673-20.0941-4.1301-2.3346
26.2457-0.9951-2.09212.6452-3.06125.5385-0.210.34080.9090.0724-0.2198-0.78120.10.24910.42980.04780.0462-0.09120.2105-0.0150.3695-6.749713.83073.3707
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A85 - 683
2X-RAY DIFFRACTION2B44 - 70

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