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- PDB-7xds: Crystal structure of wheat stem rust effector AvrSr35 -

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Basic information

Entry
Database: PDB / ID: 7xds
TitleCrystal structure of wheat stem rust effector AvrSr35
ComponentsAvrSr35
KeywordsPROTEIN TRANSPORT / Fungus / Effector / Wheat stem rust
Function / homologyAvirulence factor
Function and homology information
Biological speciesPuccinia graminis f. sp. tritici (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.06 Å
AuthorsOuyang, S.Y. / Zhao, Y.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82172287 China
CitationJournal: Sci Adv / Year: 2022
Title: Pathogen effector AvrSr35 triggers Sr35 resistosome assembly via a direct recognition mechanism.
Authors: Yan-Bo Zhao / Meng-Xi Liu / Tao-Tao Chen / Xiaomin Ma / Ze-Kai Li / Zichao Zheng / Si-Ru Zheng / Lifei Chen / You-Zhi Li / Li-Rui Tang / Qi Chen / Peiyi Wang / Songying Ouyang /
Abstract: Nucleotide-binding, leucine-rich repeat receptors (NLRs) perceive pathogen effectors to trigger plant immunity. The direct recognition mechanism of pathogen effectors by coiled-coil NLRs (CNLs) ...Nucleotide-binding, leucine-rich repeat receptors (NLRs) perceive pathogen effectors to trigger plant immunity. The direct recognition mechanism of pathogen effectors by coiled-coil NLRs (CNLs) remains unclear. We demonstrate that the CNL Sr35 directly recognizes the pathogen effector AvrSr35 from f. sp and report a cryo-electron microscopy structure of Sr35 resistosome and a crystal structure of AvrSr35. We show that AvrSr35 forms homodimers that are disassociated into monomers upon direct recognition by the leucine-rich repeat domain of Sr35, which induces Sr35 resistosome assembly and the subsequent immune response. The first 20 amino-terminal residues of Sr35 are indispensable for immune signaling but not for plasma membrane association. Our findings reveal the direct recognition and activation mechanism of a plant CNL and provide insights into biochemical function of Sr35 resistosome.
History
DepositionMar 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AvrSr35
B: AvrSr35


Theoretical massNumber of molelcules
Total (without water)133,2432
Polymers133,2432
Non-polymers00
Water1,02757
1
A: AvrSr35


Theoretical massNumber of molelcules
Total (without water)66,6211
Polymers66,6211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AvrSr35


Theoretical massNumber of molelcules
Total (without water)66,6211
Polymers66,6211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.122, 115.273, 143.162
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein AvrSr35


Mass: 66621.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Puccinia graminis f. sp. tritici (fungus)
Gene: PGT21_019944, PGTUg99_030428
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A5B0N367
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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

Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium malonate (pH 6.0), 12% (v/v) PEG 3350 / PH range: 5.6-6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.06→44.89 Å / Num. obs: 55016 / % possible obs: 97.8 % / Redundancy: 20 % / Biso Wilson estimate: 20.72 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 19
Reflection shellResolution: 2.06→2.134 Å / Rmerge(I) obs: 0.142 / Num. unique obs: 55016

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.06→44.89 Å / SU ML: 0.2834 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.374
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2869 2756 5.01 %
Rwork0.2569 52227 -
obs0.2584 54983 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.13 Å2
Refinement stepCycle: LAST / Resolution: 2.06→44.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6131 0 0 57 6188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01416248
X-RAY DIFFRACTIONf_angle_d1.70258395
X-RAY DIFFRACTIONf_chiral_restr0.1047926
X-RAY DIFFRACTIONf_plane_restr0.01161051
X-RAY DIFFRACTIONf_dihedral_angle_d17.65882362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.10.33761170.32912575X-RAY DIFFRACTION97.15
2.1-2.130.34981270.30692624X-RAY DIFFRACTION100
2.13-2.170.32781430.30262544X-RAY DIFFRACTION96.97
2.17-2.220.45381090.39662314X-RAY DIFFRACTION87.06
2.22-2.270.52871150.47542463X-RAY DIFFRACTION92.57
2.27-2.320.39211410.35152548X-RAY DIFFRACTION96.97
2.32-2.380.28981240.2742581X-RAY DIFFRACTION97.94
2.38-2.440.27411470.25892628X-RAY DIFFRACTION99.64
2.44-2.510.30161470.26632618X-RAY DIFFRACTION98.68
2.51-2.60.31411250.25442639X-RAY DIFFRACTION98.68
2.6-2.690.28241420.25492632X-RAY DIFFRACTION99.93
2.69-2.80.27511420.25482630X-RAY DIFFRACTION98.93
2.8-2.920.27041450.25962594X-RAY DIFFRACTION97.54
2.92-3.080.28431480.25512628X-RAY DIFFRACTION99.32
3.08-3.270.30121430.25382666X-RAY DIFFRACTION99.43
3.27-3.520.27861470.22812665X-RAY DIFFRACTION99.58
3.52-3.880.23141460.21352620X-RAY DIFFRACTION96.98
3.88-4.440.26681390.19522714X-RAY DIFFRACTION99.86
4.44-5.590.2361600.19932675X-RAY DIFFRACTION98.1
5.59-44.890.23641490.24182869X-RAY DIFFRACTION99.05

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