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- PDB-7xe0: Cryo-EM structure of plant NLR Sr35 resistosome -

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Basic information

Entry
Database: PDB / ID: 7xe0
TitleCryo-EM structure of plant NLR Sr35 resistosome
Components
  • AvrSr35
  • Sr35
KeywordsPLANT PROTEIN / Plant immunity / NLR / resistosome
Function / homology
Function and homology information


response to other organism / ADP binding / defense response
Similarity search - Function
Virus X resistance protein-like, coiled-coil domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Leucine-rich repeat domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Avirulence factor / CNL9
Similarity search - Component
Biological speciesTriticum monococcum (einkorn wheat)
Puccinia graminis f. sp. tritici (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsOuyang, S.Y. / Zhao, Y.B. / Li, Z.K. / Liu, M.X.
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 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.2Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sr35
B: AvrSr35
C: Sr35
E: Sr35
G: Sr35
I: Sr35
D: AvrSr35
F: AvrSr35
H: AvrSr35
J: AvrSr35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)860,02515
Polymers857,48910
Non-polymers2,5365
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Sr35


Mass: 105392.203 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum monococcum (einkorn wheat) / Gene: Sr35
Production host: Insect expression vector pBlueBacmsGCB1 (others)
References: UniProt: S5ABD6
#2: Protein
AvrSr35


Mass: 66105.586 Da / Num. of mol.: 5
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
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Sr35 resistosomeCOMPLEX#1-#20MULTIPLE SOURCES
2Sr35COMPLEX#11RECOMBINANT
3AvrSr35COMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Triticum monococcum (einkorn wheat)4568
33Puccinia graminis f. sp. tritici (fungus)56615
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Insect expression vector pBlueBacmsGCB1 (others)1944740
33Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
Buffer solutionpH: 7.5
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35510 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00450635
ELECTRON MICROSCOPYf_angle_d0.6568380
ELECTRON MICROSCOPYf_dihedral_angle_d4.8396650
ELECTRON MICROSCOPYf_chiral_restr0.0457745
ELECTRON MICROSCOPYf_plane_restr0.0048580

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