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- EMDB-32126: L7-TIR-nucleic acid End State Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-32126
TitleL7-TIR-nucleic acid End State Complex
Map dataMain map. 16 unit helical reconstructed masked.
Sample
  • Complex: L7 Toll/interleukin-1 receptor (TIR) domain
    • Protein or peptide: L7 Tir domain
Function / homology
Function and homology information


induction of programmed cell death / NADP catabolic process / cGMP biosynthetic process / NAD catabolic process / purine ribonucleoside triphosphate binding / cAMP biosynthetic process / DNA catabolic process / RNA catabolic process / regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) ...induction of programmed cell death / NADP catabolic process / cGMP biosynthetic process / NAD catabolic process / purine ribonucleoside triphosphate binding / cAMP biosynthetic process / DNA catabolic process / RNA catabolic process / regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / : / Somitogenesis / myofibril / immune system process / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / cAMP binding / sarcomere / proteasome complex / ciliary basal body / Regulation of activated PAK-2p34 by proteasome mediated degradation / proteolysis involved in protein catabolic process / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / negative regulation of inflammatory response to antigenic stimulus / lipopolysaccharide binding / Hh mutants are degraded by ERAD / Degradation of AXIN / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / P-body / ADP binding / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / response to virus / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ABC-family proteins mediated transport / CDK-mediated phosphorylation and removal of Cdc6 / response to organic cyclic compound / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / defense response / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / nuclear matrix / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / double-stranded RNA binding / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / peptidase activity / positive regulation of NF-kappaB transcription factor activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / regulation of inflammatory response / double-stranded DNA binding / secretory granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / ficolin-1-rich granule lumen / response to oxidative stress / postsynapse
Similarity search - Function
Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Proteasome subunit alpha 1 / 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, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Proteasome subunit alpha 1 / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Proteasome subunit alpha type-7 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 ...Proteasome subunit alpha type-7 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / Proteasome subunit alpha type-6 / Proteasome subunit beta type-7 / Flax rust resistance protein
Similarity search - Component
Biological speciesLinum usitatissimum (flax)
Methodhelical reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsYu D / Song W / Tan EYJ / Xu C / Wu B / Schulze-Lefert P / Chai J
Funding support1 items
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, 2021-
Header (metadata) releaseJun 1, 2022-
Map releaseJun 1, 2022-
UpdateJul 6, 2022-
Current statusJul 6, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32126.png

Downloads & links

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Map

FileDownload / File: emd_32126.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map. 16 unit helical reconstructed masked.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 219.648 Å		0.86 Å/pix.
x 256 pix.
= 219.648 Å		0.86 Å/pix.
x 256 pix.
= 219.648 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.858 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.027
Minimum - Maximum-0.07370282 - 0.13659638
Average (Standard dev.)0.0011174808 (±0.005576977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 219.648 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: central slice half map

Fileemd_32126_additional_1.map
Annotationcentral slice half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: central slice half map

Fileemd_32126_additional_2.map
Annotationcentral slice half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: non-masked half map A

Fileemd_32126_half_map_1.map
Annotationnon-masked half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: non masked half map B

Fileemd_32126_half_map_2.map
Annotationnon masked half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : L7 Toll/interleukin-1 receptor (TIR) domain

EntireName: L7 Toll/interleukin-1 receptor (TIR) domain
Components
  • Complex: L7 Toll/interleukin-1 receptor (TIR) domain
    • Protein or peptide: L7 Tir domain

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Supramolecule #1: L7 Toll/interleukin-1 receptor (TIR) domain

SupramoleculeName: L7 Toll/interleukin-1 receptor (TIR) domain / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Linum usitatissimum (flax)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21 Rosseta strain

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Macromolecule #1: L7 Tir domain

MacromoleculeName: L7 Tir domain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Linum usitatissimum (flax)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: NSKDSIVNDD DDSTSEVDAI PDSTNPSGSF PSVEYDVFLS FRGPDTRKQF TDFLYHFLCY YKIHTFRDDD ELRKGKEIGP NLLRAIDQS KIYVPIISSG YADSKWCLME LAEIVRRQEE DPRRIILPIF YMVDPSDVRH QTGCYKKAFR KHANKFDGQT I QNWKDALK ...String:
NSKDSIVNDD DDSTSEVDAI PDSTNPSGSF PSVEYDVFLS FRGPDTRKQF TDFLYHFLCY YKIHTFRDDD ELRKGKEIGP NLLRAIDQS KIYVPIISSG YADSKWCLME LAEIVRRQEE DPRRIILPIF YMVDPSDVRH QTGCYKKAFR KHANKFDGQT I QNWKDALK KVGDLKGWHI GKDDEQGAIA DKVSADIWSH ISKENL

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.2 / Component - Concentration: 50.0 mM / Component - Name: PBS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Digitization - Sampling interval: 10.0 µm / Digitization - Frames/image: 5-35 / Number grids imaged: 3 / Number real images: 10637 / Average exposure time: 40.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 33.43 Å
Applied symmetry - Helical parameters - Δ&Phi: -49.3 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.08) / Number images used: 91302
CTF correctionSoftware - Name: RELION (ver. 3.08)
Segment selectionNumber selected: 2731997 / Software - Name: RELION (ver. 3.08)
Startup modelType of model: OTHER / Details: Gaussian Noise
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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