+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32121 | |||||||||
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Title | TIR-dsDNA initial state complex | |||||||||
Map data | Main map. Could serve as the reference to produce longer filamentous densities after applying helical symmetry. PDB 7X5K was fit into helical symmetry extended version of this map. | |||||||||
Sample |
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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 | Linum usitatissimum (flax) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Yu D / Song W / Tan EYJ / Xu C / Wu B / Schulze-Lefert P / Chai J | |||||||||
Funding support | 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32121.map.gz | 3.7 MB | EMDB map data format | |
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Header (meta data) | emd-32121-v30.xml emd-32121.xml | 19.5 KB 19.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32121_fsc.xml | 4.3 KB | Display | FSC data file |
Images | emd_32121.png | 61.1 KB | ||
Others | emd_32121_additional_1.map.gz emd_32121_half_map_1.map.gz emd_32121_half_map_2.map.gz | 176.1 KB 4.3 MB 4.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32121 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32121 | HTTPS FTP |
-Validation report
Summary document | emd_32121_validation.pdf.gz | 588 KB | Display | EMDB validaton report |
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Full document | emd_32121_full_validation.pdf.gz | 587.6 KB | Display | |
Data in XML | emd_32121_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | emd_32121_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32121 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32121 | HTTPS FTP |
-Related structure data
Related structure data | 7x5kMC 7vu8C 7x5lC 7x5mC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32121.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Main map. Could serve as the reference to produce longer filamentous densities after applying helical symmetry. PDB 7X5K was fit into helical symmetry extended version of this map. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.306 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: masked out dsDNA density.
File | emd_32121_additional_1.map | ||||||||||||
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Annotation | masked out dsDNA density. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_32121_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_32121_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : L7 Toll/interleukin-1 receptor (TIR) domain
Entire | Name: L7 Toll/interleukin-1 receptor (TIR) domain |
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Components |
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-Supramolecule #1: L7 Toll/interleukin-1 receptor (TIR) domain
Supramolecule | Name: L7 Toll/interleukin-1 receptor (TIR) domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Linum usitatissimum (flax) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21 Rosseta strain |
-Macromolecule #1: L7 TIR
Macromolecule | Name: L7 TIR / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Linum usitatissimum (flax) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: NSKDSIVNDD DDSTSEVDAI PDSTNPSGSF PSVEYDVFLS FRGPDTRKQF TDFLYHFLCY YKIHTFRDDD ELRKGKEIGP NLLRAIDQSK IYVPIISSGY ADSKWCLMEL AEIVRRQEED PRRIILPIFY MVDPSDVRHQ TGCYKKAFRK HANKFDGQTI QNWKDALKKV ...String: NSKDSIVNDD DDSTSEVDAI PDSTNPSGSF PSVEYDVFLS FRGPDTRKQF TDFLYHFLCY YKIHTFRDDD ELRKGKEIGP NLLRAIDQSK IYVPIISSGY ADSKWCLMEL AEIVRRQEED PRRIILPIFY MVDPSDVRHQ TGCYKKAFRK HANKFDGQTI QNWKDALKKV GDLKGWHIGK DDEQGAIADK VSADIWSHIS KENLHHHHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.2 / Component - Concentration: 20.0 mM / Component - Name: PBS |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 10.0 µm / Digitization - Frames/image: 5-35 / Number grids imaged: 1 / Number real images: 880 / Average exposure time: 40.0 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |