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- PDB-7x5k: Tir-dsDNA complex, the initial binding state -

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Basic information

Entry
Database: PDB / ID: 7x5k
TitleTir-dsDNA complex, the initial binding state
Components
  • (DNA (43-MER)) x 2
  • 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 / 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
DNA / DNA (> 10) / Flax rust resistance protein
Similarity search - Component
Biological speciesDNA molecule (others)
Linum usitatissimum (flax)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 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 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 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
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

Downloads & links

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Assembly

Deposited unit
B: DNA (43-MER)
E: DNA (43-MER)
Q: DNA (43-MER)
S: DNA (43-MER)
C: Flax rust resistance protein
A: Flax rust resistance protein
I: Flax rust resistance protein
D: Flax rust resistance protein
M: Flax rust resistance protein
F: Flax rust resistance protein
J: Flax rust resistance protein
P: Flax rust resistance protein
N: Flax rust resistance protein
G: Flax rust resistance protein
K: Flax rust resistance protein
R: Flax rust resistance protein
O: Flax rust resistance protein
H: Flax rust resistance protein
L: Flax rust resistance protein
T: Flax rust resistance protein


Theoretical massNumber of molelcules
Total (without water)429,43420
Polymers429,43420
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: DNA chain DNA (43-MER)


Mass: 13215.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues DA B 12 and DT B 13 that are next to each other in the sample sequence are not properly linked: distance between O3' and P is 4.53. This out of range distance is due to an ...Details: Residues DA B 12 and DT B 13 that are next to each other in the sample sequence are not properly linked: distance between O3' and P is 4.53. This out of range distance is due to an intermediate state of a dsDNA hydrolysis process. Likewise, for the same reason, out of range distances are shown at the same position of chain Q.
Source: (gene. exp.) DNA molecule (others) / Production host: synthetic construct (others)
#2: DNA chain DNA (43-MER)


Mass: 13242.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues DA E 12 and DT E 13 that are next to each other in the sample sequence are not properly linked: distance between O3' and P is 3.89. This out of range distance is due to an ...Details: Residues DA E 12 and DT E 13 that are next to each other in the sample sequence are not properly linked: distance between O3' and P is 3.89. This out of range distance is due to an intermediate state of a dsDNA hydrolysis process. Likewise, for the same reason, out of range distances are shown at the same position of chain S.
Source: (gene. exp.) DNA molecule (others) / Production host: synthetic construct (others)
#3: Protein
Flax rust resistance protein


Mass: 23532.344 Da / Num. of mol.: 16 / Mutation: E197G
Source method: isolated from a genetically manipulated source
Details: L7 Tir domain / Source: (gene. exp.) Linum usitatissimum (flax) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XEH4
Compound detailsResidues DA B 12 and DT B 13 that are next to each other in the sample sequence are not properly ...Residues DA B 12 and DT B 13 that are next to each other in the sample sequence are not properly linked: distance between O3' and P is 4.53. This out of range distance is due to an intermediate state of a dsDNA hydrolysis process. Likewise, for the same reason, out of range distances are shown at the same position of chain E, Q and S.

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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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1dsDNA-Tir complexCOMPLEX16 copies of L7-Tir domain binding to 2 copies of 43bp dsDNAall0RECOMBINANT
2dsDNACOMPLEX#1-#21RECOMBINANT
3TirCOMPLEX#31RECOMBINANT
Molecular weightValue: 20 kDa/nm / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21DNA molecule (others)2853804
32Linum usitatissimum (flax)4009
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21synthetic construct (others)32630
32Escherichia coli (E. coli)562
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
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 / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18rc5_3822: / Classification: refinement
EM softwareName: RELION / Version: 3.08 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 159.2 ° / Axial rise/subunit: 16.56 Å / Axial symmetry: C1
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 228796 / Symmetry type: HELICAL
Atomic model buildingB value: 215 / Protocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00527100
ELECTRON MICROSCOPYf_angle_d0.80137242
ELECTRON MICROSCOPYf_dihedral_angle_d19.60610416
ELECTRON MICROSCOPYf_chiral_restr0.0533872
ELECTRON MICROSCOPYf_plane_restr0.0044172

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