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- EMDB-27426: Avs4 bound to phage PhiV-1 portal, symmetry-expanded C1 refinemen... -

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Basic information

Entry
Database: EMDB / ID: EMD-27426
TitleAvs4 bound to phage PhiV-1 portal, symmetry-expanded C1 refinement of TPR-portal domain
Map dataAvs4 bound to phage PhiV-1 portal, symmetry-expanded C1 refinement of TPR-portal domain
Sample
  • Complex: Avs4 bound to phage PhiV-1 portal
    • Complex: Avs4
    • Complex: phage PhiV-1 portal
Biological speciesEscherichia coli (E. coli) / Escherichia phage PhiV-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 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_27426.png

Downloads & links

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Map

FileDownload / File: emd_27426.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAvs4 bound to phage PhiV-1 portal, symmetry-expanded C1 refinement of TPR-portal domain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 360 pix.
= 372.384 Å		1.03 Å/pix.
x 360 pix.
= 372.384 Å		1.03 Å/pix.
x 360 pix.
= 372.384 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0344 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.057827517 - 0.10435087
Average (Standard dev.)0.0006732642 (±0.0022343537)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 372.384 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27426_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_27426_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_27426_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Avs4 bound to phage PhiV-1 portal

EntireName: Avs4 bound to phage PhiV-1 portal
Components
  • Complex: Avs4 bound to phage PhiV-1 portal
    • Complex: Avs4
    • Complex: phage PhiV-1 portal

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Supramolecule #1: Avs4 bound to phage PhiV-1 portal

SupramoleculeName: Avs4 bound to phage PhiV-1 portal / type: complex / Chimera: Yes / ID: 1 / Parent: 0
Molecular weightTheoretical: 980 KDa

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Supramolecule #2: Avs4

SupramoleculeName: Avs4 / type: complex / Chimera: Yes / ID: 2 / Parent: 1
Source (natural)Organism: Escherichia coli (E. coli) / Strain: NCTC11132
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: phage PhiV-1 portal

SupramoleculeName: phage PhiV-1 portal / 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

Concentration1.7 mg/mL
BufferpH: 7.4
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: 31.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 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: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 679908
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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