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- EMDB-27424: Avs3 bound to PhiV-1 terminase, symmetry-expanded C1 refinement o... -

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Basic information

Entry
Database: EMDB / ID: EMD-27424
TitleAvs3 bound to PhiV-1 terminase, symmetry-expanded C1 refinement of TPR-terminase domain
Map dataAvs3 bound to PhiV-1 terminase, symmetry-expanded C1 refinement of TPR-terminase domain
Sample
  • Complex: Avs3 bound to phage PhiV-1 terminase
    • Complex: Avs3
    • Complex: phage PhiV-1 terminase
Biological speciesSalmonella enterica (bacteria) / Escherichia phage PhiV-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWilkinson ME / Gao L / Strecker J / Makarova KS / Macrae RK / Koonin EV / Zhang F
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)5DP1HL141201-04 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)2R01HG009761-05 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2022
Title: Prokaryotic innate immunity through pattern recognition of conserved viral proteins.
Authors: Linyi Alex Gao / Max E Wilkinson / Jonathan Strecker / Kira S Makarova / Rhiannon K Macrae / Eugene V Koonin / Feng Zhang /
Abstract: Many organisms have evolved specialized immune pattern-recognition receptors, including nucleotide-binding oligomerization domain-like receptors (NLRs) of the STAND superfamily that are ubiquitous in ...Many organisms have evolved specialized immune pattern-recognition receptors, including nucleotide-binding oligomerization domain-like receptors (NLRs) of the STAND superfamily that are ubiquitous in plants, animals, and fungi. Although the roles of NLRs in eukaryotic immunity are well established, it is unknown whether prokaryotes use similar defense mechanisms. Here, we show that antiviral STAND (Avs) homologs in bacteria and archaea detect hallmark viral proteins, triggering Avs tetramerization and the activation of diverse N-terminal effector domains, including DNA endonucleases, to abrogate infection. Cryo-electron microscopy reveals that Avs sensor domains recognize conserved folds, active-site residues, and enzyme ligands, allowing a single Avs receptor to detect a wide variety of viruses. These findings extend the paradigm of pattern recognition of pathogen-specific proteins across all three domains of life.
History
DepositionJun 23, 2022-
Header (metadata) releaseAug 3, 2022-
Map releaseAug 3, 2022-
UpdateAug 24, 2022-
Current statusAug 24, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27424.png

Downloads & links

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Map

FileDownload / File: emd_27424.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAvs3 bound to PhiV-1 terminase, symmetry-expanded C1 refinement of TPR-terminase domain
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 360 pix.
= 313.092 Å		0.87 Å/pix.
x 360 pix.
= 313.092 Å		0.87 Å/pix.
x 360 pix.
= 313.092 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8697 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.024108224 - 0.047879186
Average (Standard dev.)5.7369292e-05 (±0.0014642805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 313.092 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27424_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: Half map 2

Fileemd_27424_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_27424_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Avs3 bound to phage PhiV-1 terminase

EntireName: Avs3 bound to phage PhiV-1 terminase
Components
  • Complex: Avs3 bound to phage PhiV-1 terminase
    • Complex: Avs3
    • Complex: phage PhiV-1 terminase

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Supramolecule #1: Avs3 bound to phage PhiV-1 terminase

SupramoleculeName: Avs3 bound to phage PhiV-1 terminase / type: complex / Chimera: Yes / ID: 1 / Parent: 0
Molecular weightTheoretical: 1.21 MDa

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Supramolecule #2: Avs3

SupramoleculeName: Avs3 / type: complex / Chimera: Yes / ID: 2 / Parent: 1
Source (natural)Organism: Salmonella enterica (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: phage PhiV-1 terminase

SupramoleculeName: phage PhiV-1 terminase / type: complex / Chimera: Yes / ID: 3 / Parent: 1
Source (natural)Organism: Escherichia phage PhiV-1 (virus)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 177916
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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