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- PDB-9zdw: Pseudomonas phage DEV delta-gp53 mutant neck and tail (portal, he... -

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Basic information

Entry
Database: PDB / ID: 9zdw
TitlePseudomonas phage DEV delta-gp53 mutant neck and tail (portal, head-to-tail and tail tube proteins)
Components
  • gp75 tail tube
  • gp80 portal protein
  • gp83 head-to-tail
KeywordsVIRAL PROTEIN / bacteriophage / virus
Function / homology: / Phage SU10 portal protein / Uncharacterized protein / N4 gp54-like protein / Portal protein
Function and homology information
Biological speciesPseudomonas phage vB_PaeP_DEV (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBellis, N.F. / Cingolani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 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 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
PA: gp80 portal protein
TA: gp75 tail tube
AA: gp83 head-to-tail
PB: gp80 portal protein
TB: gp75 tail tube
AB: gp83 head-to-tail
PC: gp80 portal protein
TC: gp75 tail tube
AC: gp83 head-to-tail
PD: gp80 portal protein
TD: gp75 tail tube
AD: gp83 head-to-tail
PE: gp80 portal protein
TE: gp75 tail tube
AE: gp83 head-to-tail
PF: gp80 portal protein
TF: gp75 tail tube
AF: gp83 head-to-tail
PG: gp80 portal protein
TG: gp75 tail tube
AG: gp83 head-to-tail
PH: gp80 portal protein
TH: gp75 tail tube
AH: gp83 head-to-tail
PI: gp80 portal protein
TI: gp75 tail tube
AI: gp83 head-to-tail
PJ: gp80 portal protein
TJ: gp75 tail tube
AJ: gp83 head-to-tail
PK: gp80 portal protein
TK: gp75 tail tube
AK: gp83 head-to-tail
PL: gp80 portal protein
TL: gp75 tail tube
AL: gp83 head-to-tail


Theoretical massNumber of molelcules
Total (without water)1,738,50736
Polymers1,738,50736
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
gp80 portal protein


Mass: 81739.453 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeP_DEV (virus) / References: UniProt: A0A2K8IC08
#2: 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
#3: Protein
gp83 head-to-tail


Mass: 27868.934 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeP_DEV (virus) / References: UniProt: A0A2K8I0C0
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: seudomonas phage vB_PaeP_DEV / Type: VIRUS / Entity ID: all / Source: NATURAL
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
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat-2/1
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
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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
2PHENIX1.21.1_5286model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64223 / Symmetry type: POINT
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00599984
ELECTRON MICROSCOPYf_angle_d0.507135360
ELECTRON MICROSCOPYf_dihedral_angle_d11.27437728
ELECTRON MICROSCOPYf_chiral_restr0.04115084
ELECTRON MICROSCOPYf_plane_restr0.00417988

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