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- PDB-7xjp: Cryo-EM structure of EDS1 and SAG101 with ATP-APDR -

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Basic information

Entry
Database: PDB / ID: 7xjp
TitleCryo-EM structure of EDS1 and SAG101 with ATP-APDR
Components
  • Protein EDS1
  • Senescence-associated carboxylesterase 101
KeywordsPLANT PROTEIN / NLR / Plant immune signaling
Function / homology
Function and homology information


positive regulation of defense response to oomycetes / aerenchyma formation / EDS1 disease-resistance complex / positive regulation of leaf senescence / leaf abscission / systemic acquired resistance / systemic acquired resistance, salicylic acid mediated signaling pathway / plant-type hypersensitive response / response to singlet oxygen / positive regulation of defense response to bacterium ...positive regulation of defense response to oomycetes / aerenchyma formation / EDS1 disease-resistance complex / positive regulation of leaf senescence / leaf abscission / systemic acquired resistance / systemic acquired resistance, salicylic acid mediated signaling pathway / plant-type hypersensitive response / response to singlet oxygen / positive regulation of defense response to bacterium / carboxylesterase / lipase activity / carboxylesterase activity / regulation of hydrogen peroxide metabolic process / carboxylic ester hydrolase activity / lipid catabolic process / positive regulation of defense response to virus by host / chloroplast / lipid metabolic process / defense response to Gram-negative bacterium / response to hypoxia / endoplasmic reticulum / protein homodimerization activity / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Senescence-associated carboxylesterase 101-like / 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
ADENOSINE-5-DIPHOSPHORIBOSE / ADENOSINE-5'-TRIPHOSPHATE / ISOPROPYL ALCOHOL / Senescence-associated carboxylesterase 101 / Protein EDS1
Similarity search - Component
Biological speciesArabidopsis (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsHuang, S.J. / Jia, A.L. / 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: TIR-catalyzed ADP-ribosylation reactions produce signaling molecules for plant immunity.
Authors: Aolin Jia / Shijia Huang / Wen Song / Junli Wang / Yonggang Meng / Yue Sun / Lina Xu / Henriette Laessle / Jan Jirschitzka / Jiao Hou / Tiantian Zhang / Wenquan Yu / Giuliana Hessler / ...Authors: Aolin Jia / Shijia Huang / Wen Song / Junli Wang / Yonggang Meng / Yue Sun / Lina Xu / Henriette Laessle / Jan Jirschitzka / Jiao Hou / Tiantian Zhang / Wenquan Yu / Giuliana Hessler / Ertong Li / Shoucai Ma / Dongli Yu / Jan Gebauer / Ulrich Baumann / Xiaohui Liu / Zhifu Han / Junbiao Chang / Jane E Parker / Jijie Chai /
Abstract: Plant pathogen-activated immune signaling by nucleotide-binding leucine-rich repeat (NLR) receptors with an N-terminal Toll/interleukin-1 receptor (TIR) domain converges on Enhanced Disease ...Plant pathogen-activated immune signaling by nucleotide-binding leucine-rich repeat (NLR) receptors with an N-terminal Toll/interleukin-1 receptor (TIR) domain converges on Enhanced Disease Susceptibility 1 (EDS1) and its direct partners, Phytoalexin Deficient 4 (PAD4) or Senescence-Associated Gene 101 (SAG101). TIR-encoded nicotinamide adenine dinucleotide hydrolase (NADase) produces signaling molecules to promote exclusive EDS1-PAD4 and EDS1-SAG101 interactions with helper NLR subclasses. In this work, we show that TIR-containing proteins catalyze adenosine diphosphate (ADP)-ribosylation of adenosine triphosphate (ATP) and ADP ribose (ADPR) through ADPR polymerase-like and NADase activity, forming ADP-ribosylated ATP (ADPr-ATP) and ADPr-ADPR (di-ADPR), respectively. Specific binding of ADPr-ATP or di-ADPR allosterically promotes EDS1-SAG101 interaction with helper NLR N requirement gene 1A (NRG1A) in vitro and in planta. Our data reveal an enzymatic activity of TIRs that enables specific activation of the EDS1-SAG101-NRG1 immunity branch.
History
DepositionApr 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 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 / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 3, 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

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Assembly

Deposited unit
A: Protein EDS1
B: Senescence-associated carboxylesterase 101
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,0645
Polymers133,9382
Non-polymers1,1273
Water00
1


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

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Components

#1: 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 (plant) / Gene: EDS1, EDS1-90, EDS1A, At3g48090, T17F15.40 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9SU72
#2: Protein Senescence-associated carboxylesterase 101


Mass: 62153.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis (plant) / Gene: SAG101, At5g14930, F2G14.50 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q4F883, carboxylesterase
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY

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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

ComponentName: Binary complex of EDS1 and SAG101 with molecule ATP-ADPR
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis (plant)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
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: 1.15.2_3472: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 652337 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039127
ELECTRON MICROSCOPYf_angle_d0.58812325
ELECTRON MICROSCOPYf_dihedral_angle_d7.0516660
ELECTRON MICROSCOPYf_chiral_restr0.0421340
ELECTRON MICROSCOPYf_plane_restr0.0051557

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