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- PDB-9y9c: Cryo-EM map of the in vitro reconstituted RAZR:GP77 complex with ... -

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Basic information

Entry
Database: PDB / ID: 9y9c
TitleCryo-EM map of the in vitro reconstituted RAZR:GP77 complex with AlphaFold-predicted models fitted into the density.
Components
  • DUF4145 domain-containing protein
  • Gp77
KeywordsRNA BINDING PROTEIN / Phage-bacterial defense complex / Abortive infection Ring-Activated Zinc-Finger RNase (RAZR)
Function / homologyDomain of unknown function DUF4145 / Domain of unknown function (DUF4145) / DUF4145 domain-containing protein / :
Function and homology information
Biological speciesEscherichia phage SECphi27 (virus)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLyu, Y. / Zhang, T. / Laub, M. / Ghanbarpour, A.
Funding support United States, 2items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.1Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
IA: Gp77
IB: Gp77
IC: Gp77
ID: Gp77
IE: Gp77
IF: Gp77
IG: Gp77
IH: Gp77
II: Gp77
IJ: Gp77
IK: Gp77
IL: Gp77
IM: Gp77
IN: Gp77
IO: Gp77
IP: Gp77
IQ: Gp77
IR: Gp77
IS: Gp77
IT: Gp77
IU: Gp77
IV: Gp77
IW: Gp77
IX: Gp77
OA: DUF4145 domain-containing protein
OB: DUF4145 domain-containing protein
OC: DUF4145 domain-containing protein
OD: DUF4145 domain-containing protein
OE: DUF4145 domain-containing protein
OF: DUF4145 domain-containing protein
OG: DUF4145 domain-containing protein
OH: DUF4145 domain-containing protein
OI: DUF4145 domain-containing protein
OJ: DUF4145 domain-containing protein
OK: DUF4145 domain-containing protein
OL: DUF4145 domain-containing protein
OM: DUF4145 domain-containing protein
ON: DUF4145 domain-containing protein
OO: DUF4145 domain-containing protein
OP: DUF4145 domain-containing protein
OQ: DUF4145 domain-containing protein
OR: DUF4145 domain-containing protein
OS: DUF4145 domain-containing protein
OT: DUF4145 domain-containing protein
OU: DUF4145 domain-containing protein
OV: DUF4145 domain-containing protein
OW: DUF4145 domain-containing protein
OX: DUF4145 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,205,95472
Polymers1,204,38448
Non-polymers1,57024
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Gp77


Mass: 25475.650 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage SECphi27 (virus) / Gene: JLBYU38_79 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AAE8YXX1
#2: Protein ...
DUF4145 domain-containing protein


Mass: 24707.023 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: C9194_06935, DIV22_05270, DU321_12645, NY836_21110 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F3V1L6
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RazR:GP77 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 47.18 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of real images: 11152

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv.4.7.0particle selection
2Topazparticle selection
13cryoSPARC4.7.03D reconstruction
14PHENIX1.21.2_5419:model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28191 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00357958
ELECTRON MICROSCOPYf_angle_d0.68478429
ELECTRON MICROSCOPYf_dihedral_angle_d4.0557896
ELECTRON MICROSCOPYf_chiral_restr0.0418567
ELECTRON MICROSCOPYf_plane_restr0.00410344

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