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- PDB-7xc2: Cryo EM structure of oligomeric complex formed by wheat CNL Sr35 ... -

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Basic information

Entry
Database: PDB / ID: 7xc2
TitleCryo EM structure of oligomeric complex formed by wheat CNL Sr35 and the effector AvrSr35 of the wheat stem rust pathogen
Components
  • Avirulence factor
  • CNL9
KeywordsPLANT PROTEIN/INHIBITOR / LRR / CC / direct recognition / PLANT PROTEIN-INHIBITOR COMPLEX
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 Å
AuthorsAlexander, F. / Li, E.T. / Aaron, L. / Deng, Y.N. / Sun, Y. / Chai, J.J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Alexander von Humboldt Foundation Germany
CitationJournal: Nature / Year: 2022
Title: A wheat resistosome defines common principles of immune receptor channels.
Authors: Alexander Förderer / Ertong Li / Aaron W Lawson / Ya-Nan Deng / Yue Sun / Elke Logemann / Xiaoxiao Zhang / Jie Wen / Zhifu Han / Junbiao Chang / Yuhang Chen / Paul Schulze-Lefert / Jijie Chai /
Abstract: Plant intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) detect pathogen effectors to trigger immune responses. Indirect recognition of a pathogen effector by the dicotyledonous ...Plant intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) detect pathogen effectors to trigger immune responses. Indirect recognition of a pathogen effector by the dicotyledonous Arabidopsis thaliana coiled-coil domain containing NLR (CNL) ZAR1 induces the formation of a large hetero-oligomeric protein complex, termed the ZAR1 resistosome, which functions as a calcium channel required for ZAR1-mediated immunity. Whether the resistosome and channel activities are conserved among plant CNLs remains unknown. Here we report the cryo-electron microscopy structure of the wheat CNL Sr35 in complex with the effector AvrSr35 of the wheat stem rust pathogen. Direct effector binding to the leucine-rich repeats of Sr35 results in the formation of a pentameric Sr35-AvrSr35 complex, which we term the Sr35 resistosome. Wheat Sr35 and Arabidopsis ZAR1 resistosomes bear striking structural similarities, including an arginine cluster in the leucine-rich repeats domain not previously recognized as conserved, which co-occurs and forms intramolecular interactions with the 'EDVID' motif in the coiled-coil domain. Electrophysiological measurements show that the Sr35 resistosome exhibits non-selective cation channel activity. These structural insights allowed us to generate new variants of closely related wheat and barley orphan NLRs that recognize AvrSr35. Our data support the evolutionary conservation of CNL resistosomes in plants and demonstrate proof of principle for structure-based engineering of NLRs for crop improvement.
History
DepositionMar 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 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
C: CNL9
D: Avirulence factor
A: CNL9
B: Avirulence factor
E: CNL9
F: Avirulence factor
G: CNL9
H: Avirulence factor
I: CNL9
J: Avirulence factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)765,32515
Polymers762,78910
Non-polymers2,5365
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
CNL9


Mass: 102046.242 Da / Num. of mol.: 5 / Mutation: N151Q, I450V, I618V, I864S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum monococcum (einkorn wheat) / Gene: Sr35 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: S5ABD6
#2: Protein
Avirulence factor


Mass: 50511.480 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Puccinia graminis f. sp. tritici (fungus)
Gene: AvrSr35 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2I6B3G6
#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
1Cryo EM structure of oligomeric complex formed by wheat CNL Sr35 and the effector AvrSr35 of the wheat stem rust pathogenCOMPLEX#1-#20RECOMBINANT
2CNL9COMPLEX#11RECOMBINANT
3Avirulence factorCOMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Triticum monococcum (einkorn wheat)4568
32Puccinia graminis f. sp. tritici (fungus)56615
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Spodoptera frugiperda (fall armyworm)7108
32Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: DARK FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.33 CUT-OFF / Num. of particles: 230485 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00753090
ELECTRON MICROSCOPYf_angle_d0.75171685
ELECTRON MICROSCOPYf_dihedral_angle_d10.38632415
ELECTRON MICROSCOPYf_chiral_restr0.0468070
ELECTRON MICROSCOPYf_plane_restr0.0049035

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