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- EMDB-43562: Cryo-EM structure of a type I ZorAB complex from Shewanella sp. s... -

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Basic information

Entry
Database: EMDB / ID: EMD-43562
TitleCryo-EM structure of a type I ZorAB complex from Shewanella sp. strain ANA-3, PG-binding domain focused map
Map datasharpened map from PG-binding domain focused refinement
Sample
  • Complex: ZorAB complex
Keywordsphage defense / zorya / phage / membrane protein complex / MEMBRANE PROTEIN
Biological speciesShewanella sp. ANA-3 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsDeme JC / Lea SM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CCR Core Funding for Lea Group United States
CitationJournal: Nat Commun / Year: 2025
Title: Modularity of Zorya defense systems during phage inhibition.
Authors: Giuseppina Mariano / Justin C Deme / Jennifer J Readshaw / Matthew J Grobbelaar / Mackenzie Keenan / Yasmin El-Masri / Lindsay Bamford / Suraj Songra / Tim R Blower / Tracy Palmer / Susan M Lea /
Abstract: Bacteria have evolved an extraordinary diversity of defense systems against bacteriophage (phage) predation. However, the molecular mechanisms underlying these anti-phage systems often remain elusive. ...Bacteria have evolved an extraordinary diversity of defense systems against bacteriophage (phage) predation. However, the molecular mechanisms underlying these anti-phage systems often remain elusive. Here, we provide mechanistic and structural insights into Zorya phage defense systems. Using cryo-EM structural analyses, we show that the Zorya type I and II core components, ZorA and ZorB, assemble in a 5:2 complex that is similar to inner-membrane ion-driven, rotary motors that power flagellar rotation, type 9 secretion, gliding and the Ton nutrient uptake systems. The ZorAB complex has an elongated cytoplasmic tail assembled by bundling the C-termini of the five ZorA subunits. Mutagenesis demonstrates that peptidoglycan binding by the periplasmic domains of ZorB, the structured cytoplasmic tail of ZorA, and ion flow through the motor is important for function in both type I and II systems. Furthermore, we identify ZorE as the effector module of the Zorya II system, possessing nickase activity. Our work reveals the molecular basis of the activity of Zorya systems and highlights the ZorE nickase as crucial for population-wide immunity in the type II system.
History
DepositionJan 31, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43562.png

Downloads & links

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Map

FileDownload / File: emd_43562.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map from PG-binding domain focused refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 480 pix.
= 347.04 Å		0.72 Å/pix.
x 480 pix.
= 347.04 Å		0.72 Å/pix.
x 480 pix.
= 347.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.723 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-6.404385 - 9.525134
Average (Standard dev.)0.00025201228 (±0.07180249)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 347.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43562_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map from PG-binding domain focused refinement

Fileemd_43562_additional_1.map
Annotationunsharpened map from PG-binding domain focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1, PG-binding domain focused refinement

Fileemd_43562_half_map_1.map
Annotationhalf map 1, PG-binding domain focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2, PG-binding domain focused refinement

Fileemd_43562_half_map_2.map
Annotationhalf map 2, PG-binding domain focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ZorAB complex

EntireName: ZorAB complex
Components
  • Complex: ZorAB complex

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Supramolecule #1: ZorAB complex

SupramoleculeName: ZorAB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Shewanella sp. ANA-3 (bacteria)

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 587313
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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