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- PDB-7xdd: Cryo-EM structure of EDS1 and PAD4 -

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Basic information

Entry
Database: PDB / ID: 7xdd
TitleCryo-EM structure of EDS1 and PAD4
Components
  • Lipase-like PAD4
  • Protein EDS1
KeywordsTRANSFERASE/TRANSFERASE ACTIVATOR / 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 / : / systemic acquired resistance, salicylic acid mediated signaling pathway / plant-type hypersensitive response / response to salicylic acid / leaf senescence / ethylene-activated signaling pathway / 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
EDS1, EP domain / EDS1-like / Enhanced disease susceptibility 1 protein EP domain / Fungal lipase-like domain / Lipase (class 3) / Lipases, serine active site. / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Lipase-like PAD4 / Protein EDS1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsHuang, S.J. / Jia, A.L. / Sun, Y. / Han, Z.F. / Chai, J.J.
Funding support China, Germany, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Alexander von Humboldt Foundation Germany
CitationJournal: 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
DepositionMar 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 10, 2022Group: Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / em_entity_assembly_naturalsource / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_entity_assembly_naturalsource.ncbi_tax_id / _em_entity_assembly_naturalsource.organism / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipase-like PAD4
B: Protein EDS1


Theoretical massNumber of molelcules
Total (without water)132,4772
Polymers132,4772
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Lipase-like PAD4 / Protein ENHANCED DISEASE SUSCEPTIBILITY 9 / Protein PHYTOALEXIN DEFICIENT 4 / AtPAD4


Mass: 60693.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PAD4, EDS9, At3g52430, F22O6.190 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9S745, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein Protein EDS1 / Enhanced disease susceptibility 1


Mass: 71784.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: EDS1, EDS1-90, EDS1A, At3g48090, T17F15.40 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9SU72

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Binary complex of EDS1 and PAD4COMPLEXall0RECOMBINANT
2PAD4COMPLEX#11RECOMBINANT
3EDS1COMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Arabidopsis thaliana (thale cress)3702
33Arabidopsis thaliana (thale cress)3702
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Spodoptera frugiperda (fall armyworm)7108
33Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 133202 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0059227
ELECTRON MICROSCOPYf_angle_d0.59312470
ELECTRON MICROSCOPYf_dihedral_angle_d6.9411221
ELECTRON MICROSCOPYf_chiral_restr0.0431356
ELECTRON MICROSCOPYf_plane_restr0.0051602

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