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- PDB-7x5m: Tir-dsDNA complex, the initial binding state -

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Basic information

Entry
Database: PDB / ID: 7x5m
TitleTir-dsDNA complex, the initial binding state
Components
  • DNA (5'-D(P*AP*TP*TP*AP*A)-3')
  • DNA (5'-D(P*AP*TP*TP*TP*A)-3')
  • Flax rust resistance protein
KeywordsHYDROLASE/DNA / plant innate immune receptor / nucleic acids / 2' / 3'cNMP / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


induction of programmed cell death / NADP+ catabolic process / cGMP biosynthetic process / NAD+ catabolic process / cAMP biosynthetic process / DNA catabolic process / RNA catabolic process / cAMP binding / defense response / ADP binding ...induction of programmed cell death / NADP+ catabolic process / cGMP biosynthetic process / NAD+ catabolic process / cAMP biosynthetic process / DNA catabolic process / RNA catabolic process / cAMP binding / defense response / ADP binding / double-stranded RNA binding / double-stranded DNA binding / hydrolase activity / signal transduction
Similarity search - Function
Disease resistance protein Roq1-like, winged-helix domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily ...Disease resistance protein Roq1-like, winged-helix domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
2',3'- cyclic AMP / DNA / Flax rust resistance protein
Similarity search - Component
Biological speciesDNA molecule (others)
Linum usitatissimum (flax)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsTan, Y. / Xu, C. / Yu, D. / Song, W. / Wu, B. / Schulze-Lefert, P. / Chai, J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)OFIRG Singapore
CitationJournal: Cell / Year: 2022
Title: TIR domains of plant immune receptors are 2',3'-cAMP/cGMP synthetases mediating cell death.
Authors: Dongli Yu / Wen Song / Eddie Yong Jun Tan / Li Liu / Yu Cao / Jan Jirschitzka / Ertong Li / Elke Logemann / Chenrui Xu / Shijia Huang / Aolin Jia / Xiaoyu Chang / Zhifu Han / Bin Wu / Paul ...Authors: Dongli Yu / Wen Song / Eddie Yong Jun Tan / Li Liu / Yu Cao / Jan Jirschitzka / Ertong Li / Elke Logemann / Chenrui Xu / Shijia Huang / Aolin Jia / Xiaoyu Chang / Zhifu Han / Bin Wu / Paul Schulze-Lefert / Jijie Chai /
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). ...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.
History
DepositionMar 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation
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_PubMed / _citation.title
Revision 1.2Jul 6, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Jul 2, 2025Group: Data collection / Structure summary / Category: em_software / pdbx_entry_details
Item: _em_software.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(P*AP*TP*TP*AP*A)-3')
E: DNA (5'-D(P*AP*TP*TP*TP*A)-3')
B: Flax rust resistance protein
F: Flax rust resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7206
Polymers50,0624
Non-polymers6582
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3590 Å2
ΔGint-7 kcal/mol
Surface area19880 Å2

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Components

#1: DNA chain DNA (5'-D(P*AP*TP*TP*AP*A)-3')


Mass: 1503.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DNA molecule (others) / Production host: synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*TP*TP*TP*A)-3')


Mass: 1494.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DNA molecule (others) / Production host: synthetic construct (others)
#3: Protein Flax rust resistance protein


Mass: 23532.344 Da / Num. of mol.: 2 / Fragment: L7-Tir domain / Mutation: E197G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Linum usitatissimum (flax) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XEH4
#4: Chemical ChemComp-ACK / 2',3'- cyclic AMP


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P / 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: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Tir-dsDNA, End state complex / Type: COMPLEX
Details: Tir fully digested the bound dsDNA, only ssDNA left.
Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 20 kDa/nm / Experimental value: NO
Source (natural)Organism: Linum usitatissimum (flax)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: METHANE

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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: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18rc5_3822: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -49.3 ° / Axial rise/subunit: 33.43 Å / Axial symmetry: C1
3D reconstructionResolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91302
Details: resolution was estimated based on central segment of the helical density
Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0043132
ELECTRON MICROSCOPYf_angle_d0.5094261
ELECTRON MICROSCOPYf_dihedral_angle_d16.7031168
ELECTRON MICROSCOPYf_chiral_restr0.043442
ELECTRON MICROSCOPYf_plane_restr0.003510

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