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- PDB-7vu8: L7-Tir domain with bound ligand -

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Basic information

Entry
Database: PDB / ID: 7vu8
TitleL7-Tir domain with bound ligand
ComponentsFlax rust resistance protein
KeywordsHYDROLASE / Nucleic acid hydrolysis 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 / ADP binding / defense response ...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 / ADP binding / defense response / double-stranded RNA binding / double-stranded DNA binding / hydrolase activity / signal transduction
Similarity search - Function
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 / Flax rust resistance protein
Similarity search - Component
Biological speciesLinum usitatissimum (flax)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsTan, Y. / Xu, C. / Yu, D. / Song, W. / Wu, B. / Schulze-Lefert, P. / Chai, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionNov 1, 2021Deposition 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Flax rust resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8622
Polymers23,5321
Non-polymers3291
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area700 Å2
ΔGint1 kcal/mol
Surface area9930 Å2

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Components

#1: Protein Flax rust resistance protein


Mass: 23532.344 Da / Num. of mol.: 1 / 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
#2: Chemical ChemComp-ACK / 2',3'- cyclic AMP


Mass: 329.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O6P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: One centrally located TIR domain within the complex / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.2
Buffer componentName: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / 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: OTHER
Electron lensMode: BRIGHT FIELD / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 40 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 3 / Num. of real images: 10637
Image scansSampling size: 10 µm / Width: 5760 / Height: 4092

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Processing

SoftwareName: PHENIX / Version: 1.18rc5_3822: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
7PHENIX1.19.2model fitting
12RELION3D reconstruction
13PHENIX1.19.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: OTHER / Num. of particles: 91302
Details: Phenix real space refinement, based on D99 cut off value of 0.143.
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 146 / Protocol: BACKBONE TRACE / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 146.9 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0031472
ELECTRON MICROSCOPYf_angle_d0.461987
ELECTRON MICROSCOPYf_dihedral_angle_d12.911545
ELECTRON MICROSCOPYf_chiral_restr0.042204
ELECTRON MICROSCOPYf_plane_restr0.003251

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