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- EMDB-72691: Cryo-EM Map of the Copurified Ring-Activated Zinc-Finger RNase (R... -

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Basic information

Entry
Database: EMDB / ID: EMD-72691
TitleCryo-EM Map of the Copurified Ring-Activated Zinc-Finger RNase (RAZR, H154A) in Complex with Phage Protein Gp77
Map data
Sample
  • Complex: RAZR:GP77
KeywordsPhage-bacterial defense complex / Abortive infection Ring-Activated Zinc-Finger RNase (RAZR) / RNA BINDING PROTEIN
Biological speciesBL21 DE3 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhang T / Laub M / Ghanbarpour A
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM141517 United States
National Science Foundation (NSF, United States)2046778 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2026
Title: Bacterial immune activation via supramolecular assembly with phage triggers.
Authors: Tong Zhang / Yifei Lyu / Christina R Beck / Naseer Iqbal / Renee Barbosa / Alireza Ghanbarpour / Michael T Laub /
Abstract: Bacteria use diverse mechanisms to protect themselves against phages. Many antiphage systems form large oligomeric complexes, but how oligomerization is regulated during phage infection remains ...Bacteria use diverse mechanisms to protect themselves against phages. Many antiphage systems form large oligomeric complexes, but how oligomerization is regulated during phage infection remains mostly unknown. Here we demonstrate that the bacterial immunity protein ring-activated zinc-finger RNase (RAZR) assembles into an active, 24-meric ring around the circumference of large ring structures formed by two unrelated phage proteins: a putative recombinase and a portal protein. Each multi-layered, megadalton-scale complex enables RAZR to cleave RNA nonspecifically to inhibit translation and restrict phage propagation. The recognition of unrelated phage proteins that form rings with similar diameters indicates that these proteins not only bind to RAZR but also enforce a geometry crucial to activation. The lack of large ring structures in the host probably prevents auto-immunity and RAZR activation before infection. The infection-triggered oligomerization of RAZR mirrors pathogen-induced oligomerization in eukaryotic innate immune complexes, underscoring a common principle of immunity across biology.
History
DepositionSep 13, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72691.png

Downloads & links

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Map

FileDownload / File: emd_72691.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 360 pix.
= 470.88 Å		1.31 Å/pix.
x 360 pix.
= 470.88 Å		1.31 Å/pix.
x 360 pix.
= 470.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.308 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0504
Minimum - Maximum-0.2672524 - 0.5375562
Average (Standard dev.)-0.00021731964 (±0.012534665)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 470.87997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72691_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #1

Fileemd_72691_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_72691_half_map_2.map
Projections & Slices
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Sample components

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Entire : RAZR:GP77

EntireName: RAZR:GP77
Components
  • Complex: RAZR:GP77

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Supramolecule #1: RAZR:GP77

SupramoleculeName: RAZR:GP77 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: BL21 DE3 (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: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 47.6 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: 0.25 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v.4.5.3) / Type: NONE
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v.4.5.3) / Number images used: 234639
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v.4.5.3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v.4.5.3)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model

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