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- PDB-8zf0: pRib-ADP bound OsEDS1-PAD4-ADR1 complex -

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Basic information

Entry
Database: PDB / ID: 8zf0
TitlepRib-ADP bound OsEDS1-PAD4-ADR1 complex
Components
  • EDS1
  • Lipase-like PAD4
  • RPW8 domain-containing protein
KeywordsPLANT PROTEIN / ADR1 / EDS1 / PAD4 / plant immunity / pRib-ADP / NLR
Function / homology
Function and homology information


defense response / ADP binding / lipid metabolic process / nucleus / cytoplasm
Similarity search - Function
Powdery mildew resistance protein, RPW8 domain / RPW8 domain profile. / EDS1, EP domain / EDS1-like / Enhanced disease susceptibility 1 protein EP domain / Fungal lipase-like domain / Lipase (class 3) / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain ...Powdery mildew resistance protein, RPW8 domain / RPW8 domain profile. / EDS1, EP domain / EDS1-like / Enhanced disease susceptibility 1 protein EP domain / Fungal lipase-like domain / Lipase (class 3) / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Leucine-rich repeat domain superfamily / Alpha/Beta hydrolase fold / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / RPW8 domain-containing protein / EDS1 / Lipase, putative
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsXu, W.Y. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Science / Year: 2024
Title: A canonical protein complex controls immune homeostasis and multipathogen resistance.
Authors: Yue Wu / Weiying Xu / Guoyan Zhao / Ziyao Lei / Kui Li / Jiyun Liu / Shijia Huang / Junli Wang / Xiangbin Zhong / Xin Yin / Yuandong Wang / Haochen Zhang / Yang He / Zian Ye / Yonggang Meng ...Authors: Yue Wu / Weiying Xu / Guoyan Zhao / Ziyao Lei / Kui Li / Jiyun Liu / Shijia Huang / Junli Wang / Xiangbin Zhong / Xin Yin / Yuandong Wang / Haochen Zhang / Yang He / Zian Ye / Yonggang Meng / Xiaoyu Chang / Hui Lin / Xin Wang / Yuanyuan Gao / Jijie Chai / Jane E Parker / Yiwen Deng / Yu Zhang / Mingjun Gao / Zuhua He /
Abstract: The calcium (Ca) sensor ROD1 (RESISTANCE OF RICE TO DISEASES1) is a master regulator of immunity in rice. By screening suppressors of mutants, we show that ROD1 governs immune homeostasis by ...The calcium (Ca) sensor ROD1 (RESISTANCE OF RICE TO DISEASES1) is a master regulator of immunity in rice. By screening suppressors of mutants, we show that ROD1 governs immune homeostasis by surveilling the activation of a canonical immune pathway. Mutations in (), (), (), and () all abolish enhanced disease resistance of plants. OsTIR catalyzes the production of second messengers 2'-(5″-phosphoribosyl)-5'-adenosine monophosphate (pRib-AMP) and diphosphate (pRib-ADP), which trigger formation of an OsEDS1-OsPAD4-OsADR1 (EPA) immune complex. ROD1 interacts with OsTIR and inhibits its enzymatic activity, whereas mutation of leads to constitutive activation of the EPA complex. Thus, we unveil an immune network that fine-tunes immune homeostasis and multipathogen resistance in rice.
History
DepositionMay 7, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update
Revision 1.2Jan 1, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RPW8 domain-containing protein
B: EDS1
C: Lipase-like PAD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,7044
Polymers236,0653
Non-polymers6391
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein RPW8 domain-containing protein


Mass: 96140.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence reference for strain 'Oryza sativa Japonica Group' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A0E0JBT6. The author ...Details: Sequence reference for strain 'Oryza sativa Japonica Group' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A0E0JBT6. The author provided reference sequence from NCBI (id: XP_015619838.1).
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0E0JBT6
#2: Protein EDS1 / Os09g0392100 protein


Mass: 68366.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: Os09g0392100, B1175F05.21, OsJ_29238 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A3BYH7
#3: Protein Lipase-like PAD4


Mass: 71557.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: LOC_Os11g09010 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q2R9E7
#4: Chemical ChemComp-A1D8A / [(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[(2S,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate


Mass: 639.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N5O17P3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: pRib-ADP bound OsEDS1-PAD4-ADR1 complex / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Source (natural)Organism: Oryza sativa subsp. japonica (Japanese rice)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenConc.: 11.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 174833 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE

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