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- EMDB-14122: TIR-SAVED effector bound to cA3 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-14122
TitleTIR-SAVED effector bound to cA3
Map datasharpened map
Sample
  • Complex: one tier of TIR_SAVED bound to cA3
    • Protein or peptide: TIR_SAVED fusion protein
    • RNA: RNA (5'-R(P*AP*AP*A)-3')
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
Uncharacterized protein
Similarity search - Component
Biological speciesMicrobacterium ketosireducens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSpagnolo L / White MF / Hogrel G / Guild A
Funding support United Kingdom, 3 items
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, 2022-
Header (metadata) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateSep 7, 2022-
Current statusSep 7, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14122.png

Downloads & links

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Map

FileDownload / File: emd_14122.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 400 pix.
= 398.8 Å		1 Å/pix.
x 400 pix.
= 398.8 Å		1 Å/pix.
x 400 pix.
= 398.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.997 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-0.6757433 - 1.2514111
Average (Standard dev.)0.0018050702 (±0.046127062)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 398.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14122_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: local filter map

Fileemd_14122_additional_1.map
Annotationlocal filter map
Projections & Slices
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Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_14122_additional_2.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: half mapB

Fileemd_14122_half_map_1.map
Annotationhalf mapB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_14122_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : one tier of TIR_SAVED bound to cA3

EntireName: one tier of TIR_SAVED bound to cA3
Components
  • Complex: one tier of TIR_SAVED bound to cA3
    • Protein or peptide: TIR_SAVED fusion protein
    • RNA: RNA (5'-R(P*AP*AP*A)-3')

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Supramolecule #1: one tier of TIR_SAVED bound to cA3

SupramoleculeName: one tier of TIR_SAVED bound to cA3 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Microbacterium ketosireducens (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: TIR_SAVED fusion protein

MacromoleculeName: TIR_SAVED fusion protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Microbacterium ketosireducens (bacteria)
Molecular weightTheoretical: 46.815875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPDTAINPRD PVFVSYRHSD GIALAAELTW LLRAAGIPVW RDVDDLPPGD TDARLQQAID EGISGAVIII TPQIADSRVV REVEAPRLL RLHRSSPQFA LGIVNAIQTS TGVVDYDAPD RVLGMERPEL RSVDQKSASR LGLVTMARQM LWHRIAAIRP L LSASGGEL ...String:
MPDTAINPRD PVFVSYRHSD GIALAAELTW LLRAAGIPVW RDVDDLPPGD TDARLQQAID EGISGAVIII TPQIADSRVV REVEAPRLL RLHRSSPQFA LGIVNAIQTS TGVVDYDAPD RVLGMERPEL RSVDQKSASR LGLVTMARQM LWHRIAAIRP L LSASGGEL RLSLQTRNTP QVYDRTDADL DIRIRPSAHE KLPSAHGLED FAETAQFLPD AVTRAGANGV RIEGGAHLSV SI AIGAAIP STRVGPMTVV DGRGVHWVSS TEPQLPDEPR LRIVRESTIP STAPAPGRPD VAAYIDLQHP RSDAAFDNYL TEH AAELVA WQHLAPTRTG LLDAADGGTI AAEAVAHIRE LSMTNGNAVV HLMVRGPFGL AVLIGRLTNT LRVVAYEWTD SDAP DGTFM PPRYEPIVQL RASTPAGVIE RVIVADAE

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Macromolecule #2: RNA (5'-R(P*AP*AP*A)-3')

MacromoleculeName: RNA (5'-R(P*AP*AP*A)-3') / type: rna / ID: 2 / Number of copies: 4
Source (natural)Organism: Microbacterium ketosireducens (bacteria)
Molecular weightTheoretical: 942.66 Da
SequenceString:
AAA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Average electron dose: 46.0 e/Å2

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 596378
FSC plot (resolution estimation)

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