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- PDB-7p8k: Crystal structure of in planta processed AvrRps4 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7p8k
TitleCrystal structure of in planta processed AvrRps4 in complex with the WRKY domain of RRS1
Components
  • Avirulence protein,Avirulence proteinGene-for-gene relationship
  • Disease resistance protein RRS1
KeywordsTRANSCRIPTION / Type III secreted effector / NLR / Integrated domain
Function / homology
Function and homology information


ADP binding / defense response / sequence-specific DNA binding / DNA-binding transcription factor activity / signal transduction / ATP binding / nucleus
Similarity search - Function
: / : / Avirulence protein, C-terminal domain / WRKY domain / WRKY domain superfamily / WRKY DNA -binding domain / WRKY domain profile. / DNA binding domain / Leucine-rich repeat 3 / Leucine Rich Repeat ...: / : / Avirulence protein, C-terminal domain / WRKY domain / WRKY domain superfamily / WRKY DNA -binding domain / WRKY domain profile. / DNA binding domain / Leucine-rich repeat 3 / Leucine Rich Repeat / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine-rich repeat domain superfamily / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Disease resistance protein RRS1 / Avirulence protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Pseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsMukhi, N. / Brown, H. / Gorenkin, D. / Ding, P. / Bentham, A.R. / Jones, J.D.G. / Banfield, M.J.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
European Research Council (ERC)669926 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011216/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012574 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/J/000PR9795 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Perception of structurally distinct effectors by the integrated WRKY domain of a plant immune receptor.
Authors: Mukhi, N. / Brown, H. / Gorenkin, D. / Ding, P. / Bentham, A.R. / Stevenson, C.E.M. / Jones, J.D.G. / Banfield, M.J.
History
DepositionJul 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author / database_2
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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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
B: Disease resistance protein RRS1
A: Avirulence protein,Avirulence protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4573
Polymers19,3922
Non-polymers651
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-4 kcal/mol
Surface area8610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.607, 105.607, 66.987
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Disease resistance protein RRS1 / / Disease resistance protein RCH2 / Probable WRKY transcription factor 52 / Resistance to ...Disease resistance protein RCH2 / Probable WRKY transcription factor 52 / Resistance to Colletotrichum higginsianum 2 protein / Resistance to Ralstonia solanacearum 1 protein


Mass: 9294.553 Da / Num. of mol.: 1 / Mutation: No
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RRS1, RCH2, RRS1-R, WRKY52 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle / References: UniProt: C4B7M5
#2: Protein Avirulence protein,Avirulence protein / Gene-for-gene relationship


Mass: 10097.181 Da / Num. of mol.: 1 / Mutation: No
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Gene: avrRps4 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle / References: UniProt: Q52432
#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 / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8M Potassium sodium tartrate tertrahydrate, 0.1M Sodium HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91188 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91188 Å / Relative weight: 1
ReflectionResolution: 2.65→45.77 Å / Num. obs: 6800 / % possible obs: 99.9 % / Redundancy: 20.8 % / CC1/2: 1 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.019 / Rrim(I) all: 0.097 / Net I/σ(I): 17.4
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
2.65-2.7821.91.185194138880.9040.2381.2112.3100
8.79-45.7316.70.031381322910.0070.03257.598.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B6X, 5W3X

4b6x

5w3x


Resolution: 2.65→45.77 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.919 / SU B: 33.631 / SU ML: 0.31 / SU R Cruickshank DPI: 0.4311 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.431 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2838 299 4.4 %RANDOM
Rwork0.2454 ---
obs0.2473 6477 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 173.5 Å2 / Biso mean: 93.11 Å2 / Biso min: 73.46 Å2
Baniso -1Baniso -2Baniso -3
1-3.25 Å21.63 Å20 Å2
2--3.25 Å2-0 Å2
3----10.55 Å2
Refinement stepCycle: final / Resolution: 2.65→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1016 0 1 3 1020
Biso mean--90.94 78.87 -
Num. residues----126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0131034
X-RAY DIFFRACTIONr_bond_other_d0.0010.017968
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.6551394
X-RAY DIFFRACTIONr_angle_other_deg1.1441.5962212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5855124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63821.14370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65215180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7641512
X-RAY DIFFRACTIONr_chiral_restr0.0490.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021197
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02267
LS refinement shellResolution: 2.651→2.72 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.451 19 -
Rwork0.353 467 -
all-486 -
obs--100 %
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)
18.40230.1236-2.51363.68711.92175.6965-0.05280.0757-0.42580.2830.2887-0.10560.52510.3921-0.23590.08620.10660.02870.160.08950.173649.3828-20.6583-0.0356
210.06480.81983.64294.72421.46653.6987-0.2279-0.01280.43060.12380.287-0.0364-0.13830.6671-0.05910.05860.03240.07070.24460.02040.158848.5794-3.71235.4607
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1210 - 1301
2X-RAY DIFFRACTION2A153 - 214

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