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- EMDB-39411: Cryo-EM structure of NRG1A(LRR) in complex with EDS1-SAG101-(ADPr-ATP) -
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Open data
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Basic information
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Title | Cryo-EM structure of NRG1A(LRR) in complex with EDS1-SAG101-(ADPr-ATP) | |||||||||
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![]() | Plant immunity / ETI / NRG1A / EDS1 / SAG101 / ADPr-ATP / PLANT PROTEIN / PLANT PROTEIN-HYDROLASE complex | |||||||||
Function / homology | ![]() positive regulation of defense response to oomycetes / positive regulation of leaf senescence / aerenchyma formation / EDS1 disease-resistance complex / leaf abscission / systemic acquired resistance, salicylic acid mediated signaling pathway / systemic acquired resistance / plant-type hypersensitive response / response to singlet oxygen / positive regulation of defense response to bacterium ...positive regulation of defense response to oomycetes / positive regulation of leaf senescence / aerenchyma formation / EDS1 disease-resistance complex / leaf abscission / systemic acquired resistance, salicylic acid mediated signaling pathway / systemic acquired resistance / plant-type hypersensitive response / response to singlet oxygen / positive regulation of defense response to bacterium / lipase activity / carboxylesterase / regulation of hydrogen peroxide metabolic process / carboxylesterase activity / carboxylic ester hydrolase activity / lipid catabolic process / positive regulation of defense response to virus by host / endomembrane system / chloroplast / defense response / ADP binding / lipid metabolic process / defense response to Gram-negative bacterium / response to hypoxia / endoplasmic reticulum / protein homodimerization activity / ATP binding / nucleus / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.09 Å | |||||||||
![]() | Huang S / Xiao Y / Chai J | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Balanced plant helper NLR activation by a modified host protein complex. Authors: Shijia Huang / Junli Wang / Ridan Song / Aolin Jia / Yu Xiao / Yue Sun / Lin Wang / Dennis Mahr / Zhongshou Wu / Zhifu Han / Xin Li / Jane E Parker / Jijie Chai / ![]() ![]() ![]() Abstract: Nucleotide-binding leucine-rich repeat (NLR) receptors play crucial roles in plant immunity by sensing pathogen effectors. In Arabidopsis, certain sensor NLRs function as NADases to catalyse the ...Nucleotide-binding leucine-rich repeat (NLR) receptors play crucial roles in plant immunity by sensing pathogen effectors. In Arabidopsis, certain sensor NLRs function as NADases to catalyse the production of second messengers, which can be recognized by enhanced disease susceptibility 1 (EDS1) with its partner senescence-associated gene 101 (SAG101), to activate helper NLR N requirement gene 1 (NRG1). A cryoelectron microscopy structure shows that second-messenger-activated EDS1-SAG101 mainly contacts the leucine-rich repeat domain of NRG1A to mediate the formation of an induced EDS1-SAG101-NRG1A complex. Structural comparisons show that binding of a second messenger induces conformational changes in EDS1-SAG101, which are recognized by NRG1A, leading to its allosteric activation. We further show that an inhibitory NRG1 family member, NRG1C, efficiently outcompetes NRG1A for binding to second-messenger-activated EDS1-SAG101. These findings uncover mechanisms for NRG1A activation through its recognition of a modified host EDS1-SAG101 complex, and NRG1A inhibition by NRG1C through sequestration of the activated EDS1-SAG101, thus shedding light on the activation and constraint of a central plant immune response system. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 4.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.2 KB 21.2 KB | Display Display | ![]() |
Images | ![]() | 119.6 KB | ||
Filedesc metadata | ![]() | 7.1 KB | ||
Others | ![]() ![]() | 40.8 MB 40.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8yn1MC ![]() 8yn0C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_39411_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_39411_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Ternary complex of NRG1A(LRR) with EDS1-SAG101-(ADPr-ATP)
Entire | Name: Ternary complex of NRG1A(LRR) with EDS1-SAG101-(ADPr-ATP) |
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Components |
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-Supramolecule #1: Ternary complex of NRG1A(LRR) with EDS1-SAG101-(ADPr-ATP)
Supramolecule | Name: Ternary complex of NRG1A(LRR) with EDS1-SAG101-(ADPr-ATP) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Protein EDS1
Macromolecule | Name: Protein EDS1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 70.715953 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: AFEALTGING DLITRSWSAS KQAYLTERYH KEEAGAVVIF AFQPSFSEKD FFDPDNKSSF GEIKLNRVQF PCMRKIGKGD VATVNEAFL KNLEAIIDPR TSFQASVEMA VRSRKQIVFT GHSSGGATAI LATVWYLEKY FIRNPNVYLE PRCVTFGAPL V GDSIFSHA ...String: AFEALTGING DLITRSWSAS KQAYLTERYH KEEAGAVVIF AFQPSFSEKD FFDPDNKSSF GEIKLNRVQF PCMRKIGKGD VATVNEAFL KNLEAIIDPR TSFQASVEMA VRSRKQIVFT GHSSGGATAI LATVWYLEKY FIRNPNVYLE PRCVTFGAPL V GDSIFSHA LGREKWSRFF VNFVSRFDIV PRIMLARKAS VEETLPHVLA QLDPRKSSVQ ESEQRITEFY TRVMRDTSTV AN QAVCELT GSAEAFLETL SSFLELSPYR PAGTFVFSTE KRLVAVNNSD AILQMLFYTS QASDEQEWSL IPFRSIRDHH SYE ELVQSM GKKLFNHLDG ENSIESTLND LGVSTRGRQY VQAALEEEKK RVENQKKIIQ VIEQERFLKK LAWIEDEYKP KCQA HKNGY YDSFKVSNEE NDFKANVKRA ELAGVFDEVL GLMKKCQLPD EFEGDIDWIK LATRYRRLVE PLDIANYHRH LKNED TGPY MKRGRPTRYI YAQRGYEHYI LKPNGMIAED VFWNKVNGLN LGLQLEEIQE TLKNSGSECG SCFWAEVEEL KGKPYE EVE VRVKTLEGML GEWITDGEVD DKEIFLEGST FRKWWITLPK NHKSHSPLRD Y UniProtKB: Protein EDS1 |
-Macromolecule #2: Senescence-associated carboxylesterase 101
Macromolecule | Name: Senescence-associated carboxylesterase 101 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: carboxylesterase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 61.677875 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SSSSLKGSAL GKLVVTSGLL HSSWSKILEI HNPPYSNHDP GLQVSKKKKD SGLEFQIHRE EKFTLVVFSA PPICRSSSSD STLLHVKDK ENPFPFLCSE NNPSFSLHTP AFNLFTSAST SLTYLKSELL QTLKSEKPVI ITGAALGGSV ASLYTLWLLE T IEPTLKRP ...String: SSSSLKGSAL GKLVVTSGLL HSSWSKILEI HNPPYSNHDP GLQVSKKKKD SGLEFQIHRE EKFTLVVFSA PPICRSSSSD STLLHVKDK ENPFPFLCSE NNPSFSLHTP AFNLFTSAST SLTYLKSELL QTLKSEKPVI ITGAALGGSV ASLYTLWLLE T IEPTLKRP LCITFGSPLI GDASLQQILE NSVRNSCFLH VVSAQTRIKM DFFKPFGTFL ICFDSGCVCI EDHVAVTELL NG VHDSGLV DYSQVLNRLD QSMLSLADSR LIPEDVIKGI EKRAEMKNLR FDMMFKKLND MKISMAYIEW YKKKCKEVKI GYY DRFKTQ LAFPSKEFDI NIKNHHKSEL NRFWKSVVEE VERRPQSDAS ILKRRFLFSG NNYRRMIEPL DIAEYYLEGR KEYR TTGRS HHYVMLEKWF GMESILIEKE RCKKRDLSDL LTFDSCFWAE VEDSLIVINQ LNTTVGMRDD VREVLTRKLV EFEGY VWEI ITKREVSPEI FLEESSFMKW WKEYKKIKGF NSSYLTEFMN TRKYESYGK UniProtKB: Senescence-associated carboxylesterase 101 |
-Macromolecule #3: Probable disease resistance protein At5g66900
Macromolecule | Name: Probable disease resistance protein At5g66900 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 46.461461 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SFDALDPNLK ECFLDMGSFL EDQKIRASVI IDMWVELYGK GSSILYMYLE DLASQNLLKL VPLGTNEHED GFYNDFLVTQ HDILRELAI CQSEFKENLE RKRLNLEILE NTFPDWCLNT INASLLSIST DDLFSSKWLE MDCPNVEALV LNLSSSDYAL P SFISGMKK ...String: SFDALDPNLK ECFLDMGSFL EDQKIRASVI IDMWVELYGK GSSILYMYLE DLASQNLLKL VPLGTNEHED GFYNDFLVTQ HDILRELAI CQSEFKENLE RKRLNLEILE NTFPDWCLNT INASLLSIST DDLFSSKWLE MDCPNVEALV LNLSSSDYAL P SFISGMKK LKVLTITNHG FYPARLSNFS CLSSLPNLKR IRLEKVSITL LDIPQLQLSS LKKLSLVMCS FGEVFYDTED IV VSNALSK LQEIDIDYCY DLDELPYWIS EIVSLKTLSI TNCNKLSQLP EAIGNLSRLE VLRLCSSMNL SELPEATEGL SNL RFLDIS HCLGLRKLPQ EIGKLQNLKK ISMRKCSGCE LPESVTNLEN LEVKCDEETG LLWERLKPKM RNLRVQEEEI EHNL NLLQM F UniProtKB: Probable disease resistance protein At5g66900 |
-Macromolecule #4: ADENOSINE-5-DIPHOSPHORIBOSE
Macromolecule | Name: ADENOSINE-5-DIPHOSPHORIBOSE / type: ligand / ID: 4 / Number of copies: 1 / Formula: APR |
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Molecular weight | Theoretical: 559.316 Da |
Chemical component information | ![]() ChemComp-APR: |
-Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 275262 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |