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- EMDB-33112: Cryo EM structure of oligomeric complex formed by wheat CNL Sr35 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-33112
TitleCryo EM structure of oligomeric complex formed by wheat CNL Sr35 and the effector AvrSr35 of the wheat stem rust pathogen
Map data
Sample
  • Complex: Cryo EM structure of oligomeric complex formed by wheat CNL Sr35 and the effector AvrSr35 of the wheat stem rust pathogen
    • Complex: CNL9
      • Protein or peptide: CNL9
    • Complex: Avirulence factor
      • Protein or peptide: Avirulence factor
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
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
Avirulence factor / CNL9
Similarity search - Component
Biological speciesTriticum monococcum (einkorn wheat) / Puccinia graminis f. sp. tritici (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsAlexander F / Li ET / Aaron L / Deng YN / Sun Y / Chai JJ
Funding support Germany, 1 items
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, 2022-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateNov 2, 2022-
Current statusNov 2, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33112.png

Downloads & links

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Map

FileDownload / File: emd_33112.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.020365896 - 0.09423005
Average (Standard dev.)0.00029682313 (±0.0022444017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33112_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33112_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo EM structure of oligomeric complex formed by wheat CNL Sr35 ...

EntireName: Cryo EM structure of oligomeric complex formed by wheat CNL Sr35 and the effector AvrSr35 of the wheat stem rust pathogen
Components
  • Complex: Cryo EM structure of oligomeric complex formed by wheat CNL Sr35 and the effector AvrSr35 of the wheat stem rust pathogen
    • Complex: CNL9
      • Protein or peptide: CNL9
    • Complex: Avirulence factor
      • Protein or peptide: Avirulence factor
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Cryo EM structure of oligomeric complex formed by wheat CNL Sr35 ...

SupramoleculeName: Cryo EM structure of oligomeric complex formed by wheat CNL Sr35 and the effector AvrSr35 of the wheat stem rust pathogen
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Triticum monococcum (einkorn wheat)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #2: CNL9

SupramoleculeName: CNL9 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Puccinia graminis f. sp. tritici (fungus)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #3: Avirulence factor

SupramoleculeName: Avirulence factor / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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Macromolecule #1: CNL9

MacromoleculeName: CNL9 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Triticum monococcum (einkorn wheat)
Molecular weightTheoretical: 102.046242 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: TITLEKKVRK GIESLITELK LMQAVLSKVS KVPADQLDEG VKIWAGNVKE LSYQMEDIVD AFMVRVGDGG ESTNPKNRVK KILKKVKKL FKNGKDLHRI SAALEEVVLQ AKQLAELRQR YEQEMRDTSA QTSVDPRMMA LYTDVTELVG IEETRDKLIN M LTEGDDWS ...String:
TITLEKKVRK GIESLITELK LMQAVLSKVS KVPADQLDEG VKIWAGNVKE LSYQMEDIVD AFMVRVGDGG ESTNPKNRVK KILKKVKKL FKNGKDLHRI SAALEEVVLQ AKQLAELRQR YEQEMRDTSA QTSVDPRMMA LYTDVTELVG IEETRDKLIN M LTEGDDWS KHPLKTISIV GFGGLGKTTL AKAAYDKIKV QFDCGAFVSV SRNPEMKKVL KDILYGLDKV KYENIHNAAR DE KYLIDDI IEFLNDKRYL IVIDDIWNEK AWELIKCAFS KKSPGSRLIT TTRNVSVSEA CCSSEDDIYR MEPLSNDVSR TLF CKRIFS QEEGCPQELL KVSEEILKKC GGVPLAIITI ASLLANKGHI KAKDEWYALL SSIGHGLTKN RSLEQMKKIL LFSY YDLPS YLKPCLLYLS IFPEDREIRR ARLVWRWISE GFVYSEKQDI SLYELGDSYF NELVNRSMIQ PIGIDDEGKV KACRV HDMV LDLICSLSSE ENFVTILDDP RRKMPNSESK VRRLSIQNSK IDVDTTRMEH MRSVTVFSDN VVGKVLDISR FKVLRV LDL EGCHVSDVGY VGNLLHLRYL GLKGTHVKDL PMEVGKLQFL LTLDLRGTKI EVLPWSVVQL RRLMCLYVDY GMKLPSG IG NLTFLEVLDD LGLSDVDLDF VKELGRLTKL RVLRLDFHGF DQSMGKALEE SISNMYKLDS LDVFVNRGLI NCLSEHWV P PPRLCRLAFP SKRSWFKTLP SWINPSSLPL LSYLDITLFE VRSEDIQLLG TLPALVYLEI WNYSVFEEAH EVEAPVLSS GAALFPCATE CRFIGIGAVP SMFPQGAAPR LKRLWFTFPA KWSSSENIGL GMRHLPSLQR VVVDVISEGA SREEADEAEA ALRAAAEDH PNRPILDIW

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Macromolecule #2: Avirulence factor

MacromoleculeName: Avirulence factor / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Puccinia graminis f. sp. tritici (fungus)
Molecular weightTheoretical: 50.51148 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: VNFPFPKKMI TESNSKDIRE YLASTFPFEQ QSTILDSVKS IAKVQIDDRK AFDLQLKFRQ ENLAELKDQI ILSLGANNGN QNWQKLLDY TNKLDELSNT KISPEEFIEE IQKVLYKVKL ESTSTSKLYS QFNLSIQDFA LQIIHSKYKS NQISQNDLLK L ITEDEMLK ...String:
VNFPFPKKMI TESNSKDIRE YLASTFPFEQ QSTILDSVKS IAKVQIDDRK AFDLQLKFRQ ENLAELKDQI ILSLGANNGN QNWQKLLDY TNKLDELSNT KISPEEFIEE IQKVLYKVKL ESTSTSKLYS QFNLSIQDFA LQIIHSKYKS NQISQNDLLK L ITEDEMLK ILAKTKVLTY KMKYFDSASK MGINKYISTE MMDLDWQFSH YKTFNDALKK NKASDSSYLG WLTHGYSIKY GL SPNNERS MFFQDGRKYA ELYAFSKSPH RKIIPGEHLK DLLAKINKSK GIFLDQNALL DKRIYAFHEL NTLETHFPGI TSS FTDDLK SNYRKKMESV SLTCQVLQEI GNIHRFIESK VPYHSSTEYG LFSIPKIFSI PIDYKHGEKE NLVSYVDFLY STAH ERILQ DNSINQLCLD PLQESLNRIK SNIPVFFNL

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 5 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.33 CUT-OFF / Number images used: 230485

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