[English] 日本語
Yorodumi
- PDB-8yn0: Crystal structure of NRG1C in complex with EDS1-SAG101-(ADPr-ATP) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8yn0
TitleCrystal structure of NRG1C in complex with EDS1-SAG101-(ADPr-ATP)
Components
  • Probable disease resistance protein At5g66890
  • Protein EDS1
  • Senescence-associated carboxylesterase 101
KeywordsPLANT PROTEIN/HYDROLASE / EDS1 / SAG101 / ATP-ADPR / NRG1C / PLANT PROTEIN / PLANT PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


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 / defense response to other organism / response to singlet oxygen ...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 / defense response to other organism / 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 / chloroplast / lipid metabolic process / defense response to Gram-negative bacterium / response to hypoxia / endoplasmic reticulum / protein homodimerization activity / nucleus / membrane / cytosol / cytoplasm
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. / : / Leucine-rich repeat region / Leucine-rich repeat domain superfamily ...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. / : / Leucine-rich repeat region / Leucine-rich repeat domain superfamily / Alpha/Beta hydrolase fold / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / ADENOSINE-5'-TRIPHOSPHATE / Senescence-associated carboxylesterase 101 / Probable disease resistance protein At5g66890 / Protein EDS1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsHuang, S. / Xiao, Y. / Chai, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2025
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
DepositionMar 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 26, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Protein EDS1
E: Senescence-associated carboxylesterase 101
C: Senescence-associated carboxylesterase 101
H: Probable disease resistance protein At5g66890
A: Protein EDS1
D: Probable disease resistance protein At5g66890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)363,57010
Polymers361,4376
Non-polymers2,1334
Water12,683704
1
B: Protein EDS1
E: Senescence-associated carboxylesterase 101
H: Probable disease resistance protein At5g66890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,7855
Polymers180,7183
Non-polymers1,0662
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-37 kcal/mol
Surface area65790 Å2
MethodPISA
2
C: Senescence-associated carboxylesterase 101
A: Protein EDS1
D: Probable disease resistance protein At5g66890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,7855
Polymers180,7183
Non-polymers1,0662
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-35 kcal/mol
Surface area65750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.521, 154.914, 171.110
Angle α, β, γ (deg.)90.00, 89.69, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 3 types, 6 molecules BAECHD

#1: Protein Protein EDS1 / Enhanced disease susceptibility 1


Mass: 71093.438 Da / Num. of mol.: 2
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
#2: Protein Senescence-associated carboxylesterase 101


Mass: 62022.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SAG101, At5g14930, F2G14.50 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q4F883, carboxylesterase
#3: Protein Probable disease resistance protein At5g66890


Mass: 47602.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g66890, MUD21.15 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9FKZ2

-
Non-polymers , 3 types, 708 molecules

#4: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 704 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 5% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.1 M HEPES pH 7.5, 10 % w/v Polyethylene glycol 10000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 159460 / % possible obs: 96.1 % / Redundancy: 3 % / Rrim(I) all: 0.15 / Net I/σ(I): 9.1
Reflection shellResolution: 2.49→2.54 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7943 / Rrim(I) all: 0.99

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→39.77 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2379 1990 1.25 %
Rwork0.1986 --
obs0.1991 158980 95.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.49→39.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25204 0 132 704 26040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125880
X-RAY DIFFRACTIONf_angle_d1.44934961
X-RAY DIFFRACTIONf_dihedral_angle_d19.5083427
X-RAY DIFFRACTIONf_chiral_restr0.0693854
X-RAY DIFFRACTIONf_plane_restr0.0084446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.550.33211310.286310454X-RAY DIFFRACTION89
2.55-2.620.30281430.263811267X-RAY DIFFRACTION96
2.62-2.70.30051480.253311200X-RAY DIFFRACTION96
2.7-2.790.26931400.242511268X-RAY DIFFRACTION96
2.79-2.880.32121390.246211255X-RAY DIFFRACTION96
2.88-30.25631450.230111356X-RAY DIFFRACTION97
3-3.140.27441460.225311359X-RAY DIFFRACTION97
3.14-3.30.25131510.224311351X-RAY DIFFRACTION97
3.3-3.510.23831400.207811412X-RAY DIFFRACTION97
3.51-3.780.24141410.191811364X-RAY DIFFRACTION97
3.78-4.160.24971380.177411396X-RAY DIFFRACTION97
4.16-4.760.18221460.160711264X-RAY DIFFRACTION96
4.76-5.990.19961450.177911257X-RAY DIFFRACTION95
5.99-39.770.20971370.172310787X-RAY DIFFRACTION90

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more