7X5K | pdb_00007x5k

Tir-dsDNA complex, the initial binding state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

Validation slider image for 7X5K

This is version 1.4 of the entry. See complete history

Literature

TIR domains of plant immune receptors are 2',3'-cAMP/cGMP synthetases mediating cell death.

Yu, D.Song, W.Tan, E.Y.J.Liu, L.Cao, Y.Jirschitzka, J.Li, E.Logemann, E.Xu, C.Huang, S.Jia, A.Chang, X.Han, Z.Wu, B.Schulze-Lefert, P.Chai, J.

(2022) Cell 185: 2370-2386.e18

  • DOI: https://doi.org/10.1016/j.cell.2022.04.032
  • Primary Citation Related Structures: 
    7VU8, 7X5K, 7X5L, 7X5M

  • PubMed Abstract: 

    2',3'-cAMP is a positional isomer of the well-established second messenger 3',5'-cAMP, but little is known about the biology of this noncanonical cyclic nucleotide monophosphate (cNMP). Toll/interleukin-1 receptor (TIR) domains of nucleotide-binding leucine-rich repeat (NLR) immune receptors have the NADase function necessary but insufficient to activate plant immune responses. Here, we show that plant TIR proteins, besides being NADases, act as 2',3'-cAMP/cGMP synthetases by hydrolyzing RNA/DNA. Structural data show that a TIR domain adopts distinct oligomers with mutually exclusive NADase and synthetase activity. Mutations specifically disrupting the synthetase activity abrogate TIR-mediated cell death in Nicotiana benthamiana (Nb), supporting an important role for these cNMPs in TIR signaling. Furthermore, the Arabidopsis negative regulator of TIR-NLR signaling, NUDT7, displays 2',3'-cAMP/cGMP but not 3',5'-cAMP/cGMP phosphodiesterase activity and suppresses cell death activity of TIRs in Nb. Our study identifies a family of 2',3'-cAMP/cGMP synthetases and establishes a critical role for them in plant immune responses.


  • Organizational Affiliation
    • Institute of Biochemistry, University of Cologne, Cologne, Germany; Max Planck Institute for Plant Breeding Research, Cologne, Germany.

Macromolecule Content 

  • Total Structure Weight: 429.43 kDa 
  • Atom Count: 26,102 
  • Modeled Residue Count: 2,892 
  • Deposited Residue Count: 3,436 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Flax rust resistance protein204Linum usitatissimumMutation(s): 1 
UniProt
Find proteins for Q9XEH4 (Linum usitatissimum)
Explore Q9XEH4 
Go to UniProtKB:  Q9XEH4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XEH4
Sequence Annotations
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Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (43-MER)A [auth B],
C [auth Q]
43DNA molecule
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (43-MER)B [auth E],
D [auth S]
43DNA molecule
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.08
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Singapore)SingaporeOFIRG

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-08
    Type: Initial release
  • Version 1.1: 2022-06-15
    Changes: Database references
  • Version 1.2: 2022-07-06
    Changes: Database references
  • Version 1.3: 2024-06-26
    Changes: Data collection
  • Version 1.4: 2025-06-18
    Changes: Data collection, Structure summary