+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33144 | |||||||||
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Title | Cryo-EM structure of EDS1 and PAD4 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | NLR / Plant Protein / Plant immune signaling / TRANSFERASE-TRANSFERASE ACTIVATOR complex | |||||||||
Function / homology | Function and homology information cellular response to trehalose stimulus / regulation of salicylic acid biosynthetic process / positive regulation of camalexin biosynthetic process / positive regulation of defense response to insect / aerenchyma formation / positive regulation of salicylic acid mediated signaling pathway / EDS1 disease-resistance complex / regulation of salicylic acid mediated signaling pathway / defense response to insect / negative regulation of ethylene-activated signaling pathway ...cellular response to trehalose stimulus / regulation of salicylic acid biosynthetic process / positive regulation of camalexin biosynthetic process / positive regulation of defense response to insect / aerenchyma formation / positive regulation of salicylic acid mediated signaling pathway / EDS1 disease-resistance complex / regulation of salicylic acid mediated signaling pathway / defense response to insect / negative regulation of ethylene-activated signaling pathway / leaf abscission / negative regulation of defense response / regulation of jasmonic acid mediated signaling pathway / response to insect / systemic acquired resistance, salicylic acid mediated signaling pathway / systemic acquired resistance / plant-type hypersensitive response / response to salicylic acid / ethylene-activated signaling pathway / leaf senescence / response to singlet oxygen / positive regulation of defense response to bacterium / lipase activity / regulation of hydrogen peroxide metabolic process / response to other organism / response to UV-C / lipid catabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / chloroplast / response to bacterium / lipid metabolic process / transferase activity / defense response to Gram-negative bacterium / response to hypoxia / defense response to bacterium / endoplasmic reticulum / protein homodimerization activity / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.93 Å | |||||||||
Authors | Huang SJ / Jia AL / Sun Y / Han ZF / Chai JJ | |||||||||
Funding support | China, Germany, 2 items
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Citation | Journal: Science / Year: 2022 Title: Identification and receptor mechanism of TIR-catalyzed small molecules in plant immunity. Authors: Shijia Huang / Aolin Jia / Wen Song / Giuliana Hessler / Yonggang Meng / Yue Sun / Lina Xu / Henriette Laessle / Jan Jirschitzka / Shoucai Ma / Yu Xiao / Dongli Yu / Jiao Hou / Ruiqi Liu / ...Authors: Shijia Huang / Aolin Jia / Wen Song / Giuliana Hessler / Yonggang Meng / Yue Sun / Lina Xu / Henriette Laessle / Jan Jirschitzka / Shoucai Ma / Yu Xiao / Dongli Yu / Jiao Hou / Ruiqi Liu / Huanhuan Sun / Xiaohui Liu / Zhifu Han / Junbiao Chang / Jane E Parker / Jijie Chai / Abstract: Plant nucleotide-binding leucine-rich repeat-containing (NLR) receptors with an N-terminal Toll/interleukin-1 receptor (TIR) domain sense pathogen effectors to enable TIR-encoded nicotinamide adenine ...Plant nucleotide-binding leucine-rich repeat-containing (NLR) receptors with an N-terminal Toll/interleukin-1 receptor (TIR) domain sense pathogen effectors to enable TIR-encoded nicotinamide adenine dinucleotide hydrolase (NADase) activity for immune signaling. TIR-NLR signaling requires the helper NLRs N requirement gene 1 (NRG1), Activated Disease Resistance 1 (ADR1), and Enhanced Disease Susceptibility 1 (EDS1), which forms a heterodimer with each of its paralogs Phytoalexin Deficient 4 (PAD4) and Senescence-Associated Gene 101 (SAG101). Here, we show that TIR-containing proteins catalyze the production of 2'-(5''-phosphoribosyl)-5'-adenosine monophosphate (pRib-AMP) and diphosphate (pRib-ADP) in vitro and in planta. Biochemical and structural data demonstrate that EDS1-PAD4 is a receptor complex for pRib-AMP and pRib-ADP, which allosterically promote EDS1-PAD4 interaction with ADR1-L1 but not NRG1A. Our study identifies TIR-catalyzed pRib-AMP and pRib-ADP as a missing link in TIR signaling through EDS1-PAD4 and as likely second messengers for plant immunity. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33144.map.gz | 7.7 MB | EMDB map data format | |
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Header (meta data) | emd-33144-v30.xml emd-33144.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
Images | emd_33144.png | 27.3 KB | ||
Filedesc metadata | emd-33144.cif.gz | 6.1 KB | ||
Others | emd_33144_half_map_1.map.gz emd_33144_half_map_2.map.gz | 80.8 MB 80.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33144 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33144 | HTTPS FTP |
-Validation report
Summary document | emd_33144_validation.pdf.gz | 709.3 KB | Display | EMDB validaton report |
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Full document | emd_33144_full_validation.pdf.gz | 708.8 KB | Display | |
Data in XML | emd_33144_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | emd_33144_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33144 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33144 | HTTPS FTP |
-Related structure data
Related structure data | 7xddMC 7xeyC 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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-Map
File | Download / File: emd_33144.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.6746 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33144_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33144_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Binary complex of EDS1 and PAD4
Entire | Name: Binary complex of EDS1 and PAD4 |
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Components |
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-Supramolecule #1: Binary complex of EDS1 and PAD4
Supramolecule | Name: Binary complex of EDS1 and PAD4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: PAD4
Supramolecule | Name: PAD4 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
-Supramolecule #3: EDS1
Supramolecule | Name: EDS1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
-Macromolecule #1: Lipase-like PAD4
Macromolecule | Name: Lipase-like PAD4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 60.693133 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: CRFETSELQA SVMISTPLFT DSWSSCNTAN CNGSIKIHDI AGITYVAIPA VSMIQLGNLV GLPVTGDVLF PGLSSDEPLP MVDAAILKL FLQLKIKEGL ELELLGKKLV VITGHSTGGA LAAFTALWLL SQSSPPSFRV FCITFGSPLL GNQSLSTSIS R SRLAHNFC ...String: CRFETSELQA SVMISTPLFT DSWSSCNTAN CNGSIKIHDI AGITYVAIPA VSMIQLGNLV GLPVTGDVLF PGLSSDEPLP MVDAAILKL FLQLKIKEGL ELELLGKKLV VITGHSTGGA LAAFTALWLL SQSSPPSFRV FCITFGSPLL GNQSLSTSIS R SRLAHNFC HVVSIHDLVP RSSNEQFWPF GTYLFCSDKG GVCLDNAGSV RLMFNILNTT ATQNTEEHQR YGHYVFTLSH MF LKSRSFL GGSIPDNSYQ AGVALAVEAL GFSNDDTSGV LVKECIETAT RIVRAPILRS AELANELASV LPARLEIQWY KDR CDASEE QLGYYDFFKR YSLKRDFKVN MSRIRLAKFW DTVIKMVETN ELPFDFHLGK KWIYASQFYQ LLAEPLDIAN FYKN RDIKT GGHYLEGNRP KRYEVIDKWQ KGVKVPEECV RSRYASTTQD TCFWAKLEQA KEWLDEARKE SSDPQRRSLL REKIV PFES YANTLVTKKE VSLDVKAKNS SYSVWEANLK EFKCKMGYEN EIEMVVDESD AMET UniProtKB: Lipase-like PAD4 |
-Macromolecule #2: Protein EDS1
Macromolecule | Name: Protein EDS1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 71.784195 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MAFEALTGIN GDLITRSWSA SKQAYLTERY HKEEAGAVVI FAFQPSFSEK DFFDPDNKSS FGEIKLNRVQ FPCMRKIGKG DVATVNEAF LKNLEAIIDP RTSFQASVEM AVRSRKQIVF TGHSSGGATA ILATVWYLEK YFIRNPNVYL EPRCVTFGAP L VGDSIFSH ...String: MAFEALTGIN GDLITRSWSA SKQAYLTERY HKEEAGAVVI FAFQPSFSEK DFFDPDNKSS FGEIKLNRVQ FPCMRKIGKG DVATVNEAF LKNLEAIIDP RTSFQASVEM AVRSRKQIVF TGHSSGGATA ILATVWYLEK YFIRNPNVYL EPRCVTFGAP L VGDSIFSH ALGREKWSRF FVNFVSRFDI VPRIMLARKA SVEETLPHVL AQLDPRKSSV QESEQRITEF YTRVMRDTST VA NQAVCEL TGSAEAFLET LSSFLELSPY RPAGTFVFST EKRLVAVNNS DAILQMLFYT SQASDEQEWS LIPFRSIRDH HSY EELVQS MGKKLFNHLD GENSIESTLN DLGVSTRGRQ YVQAALEEEK KRVENQKKII QVIEQERFLK KLAWIEDEYK PKCQ AHKNG YYDSFKVSNE ENDFKANVKR AELAGVFDEV LGLMKKCQLP DEFEGDIDWI KLATRYRRLV EPLDIANYHR HLKNE DTGP YMKRGRPTRY IYAQRGYEHY ILKPNGMIAE DVFWNKVNGL NLGLQLEEIQ ETLKNSGSEC GSCFWAEVEE LKGKPY EEV EVRVKTLEGM LGEWITDGEV DDKEIFLEGS TFRKWWITLP KNHKSHSPLR DYMMDEITDT UniProtKB: Protein EDS1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k 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: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133202 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |