8ZF0 | pdb_00008zf0

pRib-ADP bound OsEDS1-PAD4-ADR1 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A canonical protein complex controls immune homeostasis and multipathogen resistance.

Wu, Y.Xu, W.Zhao, G.Lei, Z.Li, K.Liu, J.Huang, S.Wang, J.Zhong, X.Yin, X.Wang, Y.Zhang, H.He, Y.Ye, Z.Meng, Y.Chang, X.Lin, H.Wang, X.Gao, Y.Chai, J.Parker, J.E.Deng, Y.Zhang, Y.Gao, M.He, Z.

(2024) Science 386: 1405-1412

  • DOI: https://doi.org/10.1126/science.adr2138
  • Primary Citation of Related Structures:  
    8ZF0

  • PubMed Abstract: 

    The Ca 2+ sensor, ROD1, is a master regulator of immunity in rice. By screening suppressors of rod1 mutants, we show that ROD1 governs immune homeostasis by surveilling the activation of a canonical immune pathway. Mutations in OsTIR ( TIR-only protein ), OsEDS1 ( Enhanced Disease Susceptibility 1 ), OsPAD4 ( Phytoalexin Deficient 4 ), and OsADR1 ( Activated Disease Resistance 1 ) all abolish enhanced disease resistance of rod1 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 while mutation of ROD1 leads to constitutive activation of the EPA complex. Thus, we unveil an immune network that fine-tunes immune homeostasis and multipathogen resistance in rice.


  • Organizational Affiliation
    • CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RPW8 domain-containing protein859Oryza sativa Japonica GroupMutation(s): 0 
UniProt
Find proteins for Q2QMY3 (Oryza sativa subsp. japonica)
Explore Q2QMY3 
Go to UniProtKB:  Q2QMY3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2QMY3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
EDS1621Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: Os09g0392100B1175F05.21OsJ_29238
UniProt
Find proteins for Q6H415 (Oryza sativa subsp. japonica)
Explore Q6H415 
Go to UniProtKB:  Q6H415
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6H415
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Lipase-like PAD4659Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: LOC_Os11g09010
UniProt
Find proteins for Q2R9E7 (Oryza sativa subsp. japonica)
Explore Q2R9E7 
Go to UniProtKB:  Q2R9E7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2R9E7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1D8A (Subject of Investigation/LOI)
Query on A1D8A

Download Ideal Coordinates CCD File 
D [auth B][(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
C15 H24 N5 O17 P3
GOABUQLPPRUQSR-ZQSHOCFMSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Data collection, Database references
  • Version 1.2: 2025-01-01
    Changes: Data collection, Database references