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- EMDB-33153: Cryo-EM structure of plant NLR Sr35 resistosome -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-33153
TitleCryo-EM structure of plant NLR Sr35 resistosome
Map data
Sample
  • Complex: Sr35 resistosome
    • Complex: Sr35
      • Protein or peptide: Sr35
    • Complex: AvrSr35
      • Protein or peptide: AvrSr35
  • 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: 3.33 Å
AuthorsOuyang SY / Zhao YB / Li ZK / Liu MX
Funding support China, 1 items
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, 2022-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateOct 5, 2022-
Current statusOct 5, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33153.png

Downloads & links

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Map

FileDownload / File: emd_33153.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.0068
Minimum - Maximum-0.021786701 - 0.04382453
Average (Standard dev.)4.859465e-05 (±0.0014094677)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Sr35 resistosome

EntireName: Sr35 resistosome
Components
  • Complex: Sr35 resistosome
    • Complex: Sr35
      • Protein or peptide: Sr35
    • Complex: AvrSr35
      • Protein or peptide: AvrSr35
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Sr35 resistosome

SupramoleculeName: Sr35 resistosome / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Sr35

SupramoleculeName: Sr35 / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Triticum monococcum (einkorn wheat)
Recombinant expressionOrganism: Insect expression vector pBlueBacmsGCB1 (others)

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Supramolecule #3: AvrSr35

SupramoleculeName: AvrSr35 / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Puccinia graminis f. sp. tritici (fungus)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Macromolecule #1: Sr35

MacromoleculeName: Sr35 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Triticum monococcum (einkorn wheat)
Molecular weightTheoretical: 105.392203 KDa
Recombinant expressionOrganism: Insect expression vector pBlueBacmsGCB1 (others)
SequenceString: TENLYFQSNA MEIAMGAIGS LLPKLGELLI GEITLEKKVR KGIESLITEL KLMQAVLSKV SKVPADQLDE GVKIWAGNVK ELSYQMEDI VDAFMVRVGD GGESTNPKNR VKKILKKVKK LFKNGKDLHR ISAALEEVVL QAKQLAELRQ RYEQEMRDTS A NTSVDPRM ...String:
TENLYFQSNA MEIAMGAIGS LLPKLGELLI GEITLEKKVR KGIESLITEL KLMQAVLSKV SKVPADQLDE GVKIWAGNVK ELSYQMEDI VDAFMVRVGD GGESTNPKNR VKKILKKVKK LFKNGKDLHR ISAALEEVVL QAKQLAELRQ RYEQEMRDTS A NTSVDPRM MALYTDVTEL VGIEETRDKL INMLTEGDDW SKHPLKTISI VGFGGLGKTT LAKAAYDKIK VQFDCGAFVS VS RNPEMKK VLKDILYGLD KVKYENIHNA ARDEKYLIDD IIEFLNDKRY LIVIDDIWNE KAWELIKCAF SKKSPGSRLI TTT RNVSVS EACCSSEDDI YRMEPLSNDV SRTLFCKRIF SQEEGCPQEL LKVSEEILKK CGGVPLAIIT IASLLANKGH IKAK DEWYA LLSSIGHGLT KNRSLEQMKK ILLFSYYDLP SYLKPCLLYL SIFPEDREIR RARLIWRWIS EGFVYSEKQD ISLYE LGDS YFNELVNRSM IQPIGIDDEG KVKACRVHDM VLDLICSLSS EENFVTILDD PRRKMPNSES KVRRLSIQNS KIDVDT TRM EHMRSVTVFS DNVVGKVLDI SRFKVLRVLD LEGCHVSDVG YVGNLLHLRY LGLKGTHVKD LPMEIGKLQF LLTLDLR GT KIEVLPWSVV QLRRLMCLYV DYGMKLPSGI GNLTFLEVLD DLGLSDVDLD FVKELGRLTK LRVLRLDFHG FDQSMGKA L EESISNMYKL DSLDVFVNRG LINCLSEHWV PPPRLCRLAF PSKRSWFKTL PSWINPSSLP LLSYLDITLF EVRSEDIQL LGTLPALVYL EIWNYSVFEE AHEVEAPVLS SGAALFPCAT ECRFIGIGAV PSMFPQGAAP RLKRLWFTFP AKWISSENIG LGMRHLPSL QRVVVDVISE GASREEADEA EAALRAAAED HPNRPILDIW

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Macromolecule #2: AvrSr35

MacromoleculeName: AvrSr35 / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Puccinia graminis f. sp. tritici (fungus)
Molecular weightTheoretical: 66.105586 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: HHHHHHSSGV DLGTENLYFQ SNAMRNFAAD RVHGVESVIS GSKSSSNPMA LSKSMDKPDT SDLVDSNVQA KNDGSRYEED FTAKYSEQV DHVSKILKEI EEQEPGTIII DHKAFPIQDK SPKQVVNFPF PKKMITESNS KDIREYLAST FPFEQQSTIL D SVKSIAKV ...String:
HHHHHHSSGV DLGTENLYFQ SNAMRNFAAD RVHGVESVIS GSKSSSNPMA LSKSMDKPDT SDLVDSNVQA KNDGSRYEED FTAKYSEQV DHVSKILKEI EEQEPGTIII DHKAFPIQDK SPKQVVNFPF PKKMITESNS KDIREYLAST FPFEQQSTIL D SVKSIAKV QIDDRKAFDL QLKFRQENLA ELKDQIILSL GANNGNQNWQ KLLDYTNKLD ELSNTKISPE EFIEEIQKVL YK VKLESTS TSKLYSQFNL SIQDFALQII HSKYKSNQIS QNDLLKLITE DEMLKILAKT KVLTYKMKYF DSASKMGINK YIS TEMMDL DWQFSHYKTF NDALKKNKAS DSSYLGWLTH GYSIKYGLSP NNERSMFFQD GRKYAELYAF SKSPHRKIIP GEHL KDLLA KINKSKGIFL DQNALLDKRI YAFHELNTLE THFPGITSSF TDDLKSNYRK KMESVSLTCQ VLQEIGNIHR FIESK VPYH SSTEYGLFSI PKIFSIPIDY KHGEKENLVS YVDFLYSTAH ERILQDNSIN QLCLDPLQES LNRIKSNIPV FFNLAS HSS PIKPSNVHEG KL

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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

Concentration0.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35510

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