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Yorodumi- EMDB-33486: Cryo-EM structure of binary complex of plant NLR Sr35 and effecto... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33486 | |||||||||
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Title | Cryo-EM structure of binary complex of plant NLR Sr35 and effector AvrSr35 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Plant immunity / NLR / resistosome / PLANT PROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Triticum monococcum (einkorn wheat) / Puccinia graminis f. sp. tritici (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Ouyang SY / Zhao YB / Li ZK / Liu MX | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33486.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-33486-v30.xml emd-33486.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_33486.png | 45.8 KB | ||
Filedesc metadata | emd-33486.cif.gz | 6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33486 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33486 | HTTPS FTP |
-Validation report
Summary document | emd_33486_validation.pdf.gz | 474 KB | Display | EMDB validaton report |
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Full document | emd_33486_full_validation.pdf.gz | 473.6 KB | Display | |
Data in XML | emd_33486_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_33486_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33486 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33486 | HTTPS FTP |
-Related structure data
Related structure data | 7xvgMC 7xdsC 7xe0C 7xx2C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33486.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : binary complex of Sr35 and AvrSr35
Entire | Name: binary complex of Sr35 and AvrSr35 |
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Components |
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-Supramolecule #1: binary complex of Sr35 and AvrSr35
Supramolecule | Name: binary complex of Sr35 and AvrSr35 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Sr35
Supramolecule | Name: Sr35 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Triticum monococcum (einkorn wheat) |
-Supramolecule #3: AvrSr35
Supramolecule | Name: AvrSr35 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Puccinia graminis f. sp. tritici (fungus) |
-Macromolecule #1: Sr35
Macromolecule | Name: Sr35 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Triticum monococcum (einkorn wheat) |
Molecular weight | Theoretical: 105.392203 KDa |
Recombinant expression | Organism: Insect expression vector pBlueBacmsGCB1 (others) |
Sequence | String: 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 UniProtKB: CNL9 |
-Macromolecule #2: AvrSr35
Macromolecule | Name: AvrSr35 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Puccinia graminis f. sp. tritici (fungus) |
Molecular weight | Theoretical: 51.227949 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: HHHHHHSSGV DLGTENLYFQ SNANSKDIRE YLASTFPFEQ QSTILDSVKS IAKVQIDDRK AFDLQLKFRQ ENLAELKDQI ILSLGANNG NQNWQKLLDY TNKLDELSNT KISPEEFIEE IQKVLYKVKL ESTSTSKLYS QFNLSIQDFA LQIIHSKYKS N QISQNDLL ...String: HHHHHHSSGV DLGTENLYFQ SNANSKDIRE YLASTFPFEQ QSTILDSVKS IAKVQIDDRK AFDLQLKFRQ ENLAELKDQI ILSLGANNG NQNWQKLLDY TNKLDELSNT KISPEEFIEE IQKVLYKVKL ESTSTSKLYS QFNLSIQDFA LQIIHSKYKS N QISQNDLL KLITEDEMLK ILAKTKVLTY KMKYFDSASK MGINKYISTE MMDLDWQFSH YKTFNDALKK NKASDSSYLG WL THGYSIK YGLSPNNERS MFFQDGRKYA ELYAFSKSPH RKIIPGEHLK DLLAKINKSK GIFLDQNALL DKRIYAFHEL NTL ETHFPG ITSSFTDDLK SNYRKKMESV SLTCQVLQEI GNIHRFIESK VPYHSSTEYG LFSIPKIFSI PIDYKHGEKE NLVS YVDFL YSTAHERILQ DNSINQLCLD PLQESLNRIK SNIPVF UniProtKB: Avirulence factor |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.25 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84004 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: NOT APPLICABLE |