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- PDB-7qqk: TIR-SAVED effector bound to cA3 -

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Basic information

Entry
Database: PDB / ID: 7qqk
TitleTIR-SAVED effector bound to cA3
Components
  • RNA (5'-R(P*AP*AP*A)-3')
  • TIR_SAVED fusion protein
KeywordsSIGNALING PROTEIN / Microbacterium ketosireducens TIR SAVED complex bound to cA3
Function / homology
Function and homology information


nucleobase-containing small molecule biosynthetic process / NAD catabolic process / NAD+ nucleosidase activity / signal transduction
Similarity search - Function
SMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain / TIR domain / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily
Similarity search - Domain/homology
RNA / Uncharacterized protein
Similarity search - Component
Biological speciesMicrobacterium ketosireducens (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSpagnolo, L. / White, M.F. / Hogrel, G. / Guild, A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T004789 United Kingdom
European Research Council (ERC)101018608 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_PC_17135 United Kingdom
CitationJournal: Nature / Year: 2022
Title: Cyclic nucleotide-induced helical structure activates a TIR immune effector.
Authors: Gaëlle Hogrel / Abbie Guild / Shirley Graham / Hannah Rickman / Sabine Grüschow / Quentin Bertrand / Laura Spagnolo / Malcolm F White /
Abstract: Cyclic nucleotide signalling is a key component of antiviral defence in all domains of life. Viral detection activates a nucleotide cyclase to generate a second messenger, resulting in activation of ...Cyclic nucleotide signalling is a key component of antiviral defence in all domains of life. Viral detection activates a nucleotide cyclase to generate a second messenger, resulting in activation of effector proteins. This is exemplified by the metazoan cGAS-STING innate immunity pathway, which originated in bacteria. These defence systems require a sensor domain to bind the cyclic nucleotide and are often coupled with an effector domain that, when activated, causes cell death by destroying essential biomolecules. One example is the Toll/interleukin-1 receptor (TIR) domain, which degrades the essential cofactor NAD when activated in response to infection in plants and bacteria or during programmed nerve cell death. Here we show that a bacterial antiviral defence system generates a cyclic tri-adenylate that binds to a TIR-SAVED effector, acting as the 'glue' to allow assembly of an extended superhelical solenoid structure. Adjacent TIR subunits interact to organize and complete a composite active site, allowing NAD degradation. Activation requires extended filament formation, both in vitro and in vivo. Our study highlights an example of large-scale molecular assembly controlled by cyclic nucleotides and reveals key details of the mechanism of TIR enzyme activation.
History
DepositionJan 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TIR_SAVED fusion protein
B: TIR_SAVED fusion protein
C: TIR_SAVED fusion protein
D: TIR_SAVED fusion protein
E: RNA (5'-R(P*AP*AP*A)-3')
F: RNA (5'-R(P*AP*AP*A)-3')
G: RNA (5'-R(P*AP*AP*A)-3')
H: RNA (5'-R(P*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)191,0348
Polymers191,0348
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: Protein
TIR_SAVED fusion protein


Mass: 46815.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbacterium ketosireducens (bacteria)
Gene: RS81_00402 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M2HE71
#2: RNA chain
RNA (5'-R(P*AP*AP*A)-3')


Mass: 942.660 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Microbacterium ketosireducens (bacteria)

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: one tier of TIR_SAVED bound to cA3 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Microbacterium ketosireducens (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 46 e/Å2 / Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 596378 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00513756
ELECTRON MICROSCOPYf_angle_d0.73818860
ELECTRON MICROSCOPYf_dihedral_angle_d8.3272048
ELECTRON MICROSCOPYf_chiral_restr0.0452200
ELECTRON MICROSCOPYf_plane_restr0.0072464

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