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- EMDB-72693: Cryo-EM map of the in vitro reconstituted RAZR:GP77 complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-72693
TitleCryo-EM map of the in vitro reconstituted RAZR:GP77 complex with AlphaFold-predicted models fitted into the density.
Map data
Sample
  • Complex: RazR:GP77 complex
    • Protein or peptide: Gp77
    • Protein or peptide: DUF4145 domain-containing protein
  • Ligand: ZINC ION
KeywordsPhage-bacterial defense complex / Abortive infection Ring-Activated Zinc-Finger RNase (RAZR) / RNA BINDING PROTEIN
Function / homologyDomain of unknown function DUF4145 / Domain of unknown function (DUF4145) / DUF4145 domain-containing protein / :
Function and homology information
Biological speciesEscherichia coli BL21(DE3) (bacteria) / Escherichia phage SECphi27 (virus) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLyu Y / Zhang T / Laub M / Ghanbarpour A
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/John E. Fogarty International Center (NIH/FIC)R35-GM141517 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 14, 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_72693.png

Downloads & links

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Map

FileDownload / File: emd_72693.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.49 Å/pix.
x 440 pix.
= 653.972 Å		1.49 Å/pix.
x 440 pix.
= 653.972 Å		1.49 Å/pix.
x 440 pix.
= 653.972 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4863 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0777
Minimum - Maximum-0.35850126 - 0.8280184
Average (Standard dev.)0.0005773878 (±0.016053865)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 653.972 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72693_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72693_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72693_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RazR:GP77 complex

EntireName: RazR:GP77 complex
Components
  • Complex: RazR:GP77 complex
    • Protein or peptide: Gp77
    • Protein or peptide: DUF4145 domain-containing protein
  • Ligand: ZINC ION

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Supramolecule #1: RazR:GP77 complex

SupramoleculeName: RazR:GP77 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: Gp77

MacromoleculeName: Gp77 / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage SECphi27 (virus)
Molecular weightTheoretical: 25.47565 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKLSDQFDKV LPALHKARSL FVKVKKDRQN SHLKNRYATL DSVLDAITPA LMDNELMIMQ DGERIDVSTL RVETTVMHVS GQWVKFYFD IPIVKNDPQG VGSAFTYGRR YSAAAAFGLS QADDDAQIAV KTVNDWKRDI EKCESVGELQ EVLKNAWKSS D AASKQVIR ...String:
MKLSDQFDKV LPALHKARSL FVKVKKDRQN SHLKNRYATL DSVLDAITPA LMDNELMIMQ DGERIDVSTL RVETTVMHVS GQWVKFYFD IPIVKNDPQG VGSAFTYGRR YSAAAAFGLS QADDDAQIAV KTVNDWKRDI EKCESVGELQ EVLKNAWKSS D AASKQVIR DHYEKRKAEI EIGGARGFNP AKPKENLASD AVDTPNSEKV KSQSITDFEG SSGHHHHHH

UniProtKB: UNIPROTKB: A0AAE8YXX1

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Macromolecule #2: DUF4145 domain-containing protein

MacromoleculeName: DUF4145 domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.707023 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAEYYPAVFE AEAFNCPHCG VYARQFWRRM YGSARELAQR TTEFRMSTCS HCGDDAYWYD GNMIIPAAGN VELPNPDMPD NCKSDYMEA RSIINLSPKG AAALLRLCLQ KLMVHLGEPG ENINKDIRSL VQKGLPVRIQ QAADICRIVG NQAVHPGEIS L DDDPQLAH ...String:
MAEYYPAVFE AEAFNCPHCG VYARQFWRRM YGSARELAQR TTEFRMSTCS HCGDDAYWYD GNMIIPAAGN VELPNPDMPD NCKSDYMEA RSIINLSPKG AAALLRLCLQ KLMVHLGEPG ENINKDIRSL VQKGLPVRIQ QAADICRIVG NQAVHPGEIS L DDDPQLAH GLFKLLNIIV DDRITRPKEI EAMFQSMPEG PRQGIENQDR QAREQQQAAN E

UniProtKB: DUF4145 domain-containing protein

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 24 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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) / Number real images: 11152 / Average electron dose: 47.18 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

CTF correctionType: NONE
Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 28191
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

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

PDB-9y9c:
Cryo-EM map of the in vitro reconstituted RAZR:GP77 complex with AlphaFold-predicted models fitted into the density.

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