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- PDB-9ze4: Asymmetric Tail Gating Complex of Pseudomonas Phage DEV -

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Basic information

Entry
Database: PDB / ID: 9ze4
TitleAsymmetric Tail Gating Complex of Pseudomonas Phage DEV
Components
  • N4 gp53-like protein
  • Tip attachment protein J central straight fiber domain-containing protein
  • gp75 tail tube
KeywordsVIRAL PROTEIN / virus / bacteriophage / receptor-binding protein
Function / homology: / Domain of unknown function DUF1983 / Bacteriophage tail tip fiber protein / Immunoglobulin-like fold / membrane / N4 gp53-like protein / Tip attachment protein J central straight fiber domain-containing protein / N4 gp54-like protein
Function and homology information
Biological speciesPseudomonas phage vB_PaeP_DEV (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.5 Å
AuthorsBellis, N.F. / Cingolani, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140733 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD024978 United States
CitationJournal: mBio / Year: 2026
Title: DEV phage exploits the essential LptD outer membrane protein as receptor for adsorption.
Authors: Jimena Nieto Noblecia / Nathan F Bellis / Cristian A Antichi / Shirin Aminian / Francesca Forti / Federica A Falchi / Davide Sposato / Francesco Imperi / Gino Cingolani / Federica Briani /
Abstract: bacteriophage (phage) DEV is a podovirus of the family, related to the prototypical phage N4. N4 uses the novel glycan receptor (NGR) surface glycan, presumably bound by the gp66 appendages, and ... bacteriophage (phage) DEV is a podovirus of the family, related to the prototypical phage N4. N4 uses the novel glycan receptor (NGR) surface glycan, presumably bound by the gp66 appendages, and the NGR transporter NfrA, recognized by the phage gp65 tail sheath, as receptors for adsorption. In contrast, DEV relies on the O-antigen moiety of lipopolysaccharide (LPS) as the primary receptor recognized by the gp53 long tail fibers. However, DEV can infect deep-rough strains that lack the O-antigen moiety by using another, still unknown receptor. Here, we provide evidence that the essential LPS transporter LptD serves as the DEV secondary receptor and that DEV gp54 is its cognate receptor-binding protein. gp54 is encoded within the essential operon, which also includes , the short tail fiber gene. Using cryogenic electron microscopy, AlphaFold modeling, and genetic analysis, we show that DEV gp56, gp55, and gp54 assemble into a receptor-binding fiber (RBF) positioned laterally to a previously uncharacterized tail plug protein, gp74. The DEV RBF is functionally equivalent to the N4 sheath protein gp65, which associates with the tail plug gp53. Thus, DEV and N4 both use a glycan and its surface-exposing transporter as receptors for adsorption. To our knowledge, this is the first example of a phage using an essential outer membrane protein as a receptor, with implications for phage therapy.
IMPORTANCE: phage DEV uses the O-antigen of lipopolysaccharide as its primary receptor. In this study, we found that LptD, an essential and highly conserved outer membrane protein, serves as the ...IMPORTANCE: phage DEV uses the O-antigen of lipopolysaccharide as its primary receptor. In this study, we found that LptD, an essential and highly conserved outer membrane protein, serves as the secondary receptor for DEV. This interaction is mediated by a specialized receptor-binding fiber composed of the DEV proteins , , and . We posit that the genes form a functional module, possibly disseminated via horizontal gene transfer among distantly related phages, involved in tail sealing and the regulated unplugging of the tail upon interaction with the bacterial receptor. Given the high conservation of receptor-binding proteins among phages in the DEV genus, we anticipate that other members of this genus may also use LptD as their receptor. Since are actively explored for phage therapy, insights into the interaction between DEV and its receptors could help develop more effective and targeted phage-based treatments.
History
DepositionNov 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
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Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Jan 21, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
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Revision 1.1Feb 4, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.3Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin / Data content type: EM metadata / EM metadata / Item: _citation.journal_volume / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: gp75 tail tube
B: gp75 tail tube
C: gp75 tail tube
D: gp75 tail tube
E: gp75 tail tube
F: gp75 tail tube
G: gp75 tail tube
H: gp75 tail tube
I: gp75 tail tube
J: gp75 tail tube
K: gp75 tail tube
L: gp75 tail tube
M: N4 gp53-like protein
N: Tip attachment protein J central straight fiber domain-containing protein
O: Tip attachment protein J central straight fiber domain-containing protein
P: Tip attachment protein J central straight fiber domain-containing protein


Theoretical massNumber of molelcules
Total (without water)644,67016
Polymers644,67016
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
gp75 tail tube


Mass: 35267.215 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeP_DEV (virus) / References: UniProt: A0A2K8I3N9
#2: Protein N4 gp53-like protein


Mass: 82267.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeP_DEV (virus) / References: UniProt: A0A2K8HNE9
#3: Protein Tip attachment protein J central straight fiber domain-containing protein


Mass: 46398.672 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeP_DEV (virus) / References: UniProt: A0A2K8HW65
Has protein modificationN

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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: Pseudomonas phage vB_PaeP_DEV / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudomonas phage vB_PaeP_DEV (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8241 / Symmetry type: POINT

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