+Open data
-Basic information
Entry | Database: PDB / ID: 7x5m | ||||||
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Title | Tir-dsDNA complex, the initial binding state | ||||||
Components |
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Keywords | HYDROLASE/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 / 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 | ||||||
Biological species | DNA molecule (others) Linum usitatissimum (flax) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.42 Å | ||||||
Authors | Tan, Y. / Xu, C. / Yu, D. / Song, W. / Wu, B. / Schulze-Lefert, P. / Chai, J. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x5m.cif.gz | 81 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x5m.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 7x5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x5m_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7x5m_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7x5m_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 7x5m_validation.cif.gz | 36.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/7x5m ftp://data.pdbj.org/pub/pdb/validation_reports/x5/7x5m | HTTPS FTP |
-Related structure data
Related structure data | 32126MC 7vu8C 7x5kC 7x5lC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: DNA chain | 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) | ||||
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#2: DNA chain | 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 | 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 | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Tir-dsDNA, End state complex / Type: COMPLEX Details: Tir fully digested the bound dsDNA, only ssDNA left. Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Value: 20 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Linum usitatissimum (flax) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: METHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18rc5_3822: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -49.3 ° / Axial rise/subunit: 33.43 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 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 | ||||||||||||||||||||||||
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