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- EMDB-74075: Pseudomonas phage DEV delta-gp53 mutant neck and tail (portal, he... -

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Basic information

Entry
Database: EMDB / ID: EMD-74075
TitlePseudomonas phage DEV delta-gp53 mutant neck and tail (portal, head-to-tail and tail tube proteins)
Map data
Sampleseudomonas phage vB_PaeP_DEV != Pseudomonas phage vB_PaeP_DEV

seudomonas phage vB_PaeP_DEV

  • Virus: Pseudomonas phage vB_PaeP_DEV (virus)
    • Protein or peptide: gp80 portal protein
    • Protein or peptide: gp75 tail tube
    • Protein or peptide: gp83 head-to-tail
Keywordsbacteriophage / virus / VIRAL PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBellis NF / Cingolani G
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74075.png

Downloads & links

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Map

FileDownload / File: emd_74075.map.gz / Format: CCP4 / Size: 224.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesX (Sec.)Y (Row.)Z (Col.)
1.19 Å/pix.
x 400 pix.
= 476. Å		1.19 Å/pix.
x 392 pix.
= 466.48 Å		1.19 Å/pix.
x 376 pix.
= 447.44 Å

Surface

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Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.19 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.109
Minimum - Maximum-0.3495012 - 0.67445266
Average (Standard dev.)0.0048007984 (±0.05435546)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin330308318
Dimensions392376400
Spacing400392376
CellA: 476.00003 Å / B: 466.48 Å / C: 447.44003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74075_msk_1.map
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Half map: #2

Fileemd_74075_half_map_1.map
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Half map: #1

Fileemd_74075_half_map_2.map
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Sample components

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Entire : seudomonas phage vB_PaeP_DEV

EntireName: seudomonas phage vB_PaeP_DEV
Components
  • Virus: Pseudomonas phage vB_PaeP_DEV (virus)
    • Protein or peptide: gp80 portal protein
    • Protein or peptide: gp75 tail tube
    • Protein or peptide: gp83 head-to-tail

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Supramolecule #1: Pseudomonas phage vB_PaeP_DEV

SupramoleculeName: Pseudomonas phage vB_PaeP_DEV / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2034344 / Sci species name: Pseudomonas phage vB_PaeP_DEV / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: gp80 portal protein

MacromoleculeName: gp80 portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeP_DEV (virus)
Molecular weightTheoretical: 81.739453 KDa
SequenceString: MADVDEDYLT LPNEDGDPSK RLQPEWSNAP SLAQLKQDYQ EAKQVTDEKI TQINRWLDYM HVRGEGKPKT EKGKSAVQPP TIRKQAEWR YSSLSEPFLS SPNIFEVNPV TWEDAESARQ NGLVLNQQFN TKLNKQRFID EYVRAGVDEG TIIVKVGWNY Q SRTVKEQV ...String:
MADVDEDYLT LPNEDGDPSK RLQPEWSNAP SLAQLKQDYQ EAKQVTDEKI TQINRWLDYM HVRGEGKPKT EKGKSAVQPP TIRKQAEWR YSSLSEPFLS SPNIFEVNPV TWEDAESARQ NGLVLNQQFN TKLNKQRFID EYVRAGVDEG TIIVKVGWNY Q SRTVKEQV VTYEMMPDSS EELAQIYQTA AQIREESPSE YPEIPEDVRL GLEETEANGI QVRAVPVGSE EEEREETVEN HP TVQVCDY NNIVIDPSCG SDFSKAKFLI ETFESSYAEL KADGRYKNLD KIQVEGQNLL SEPDYTGPSE GVRNFDFQDK SRK RLVVHE YWGYYDIHGD GVLHPIVATW VGAVMIRMEE NPFPDKKIPY VVVSYIPRKR DLYGESDGAL LIDNQRIIGA VTRG MIDTM ARSANGQVGV MKGALDVTNR RRFDRGENYE FNPGADPRAA VHMHTFPEIP QSAQYMINLQ QAEAESMTGV KAFNA GISG AALGDTATAV RGALDAASKR ELGILRRLSA GIIEIGRKII AMNAEFLDDV EVVRITNEHF VDIRRDDLAG NFDLKL DIS TAEEDNAKVN DLTFMLQTMG PNMDPMMAQQ IMGQIMELKK MPDFAKRIRE FQPQPDPIAQ QKAQLELMLL QAQIEAE RA RAAHYMSGAG LQDSKVGTEQ AKARALASQA DMTDLNFLEQ ESGVQQARKR ELQQAQSEAQ GKLAMLNSQL KRLDEATS A RTSQK

UniProtKB: Portal protein

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Macromolecule #2: gp75 tail tube

MacromoleculeName: gp75 tail tube / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeP_DEV (virus)
Molecular weightTheoretical: 35.267215 KDa
SequenceString: MAVEPITIAD LTEVKLDGKG ALDQLLQVTR LHLAKEHDAG RLKGQEYAAV LTGGITAVLQ NAVMFLLQKD EAANKAALVE AQIKLTEKQ GELLDKQIAQ ADKDAELIAA KVKLTLEQAK LPDSQIRSAG FQDLLVQEQT KVQTAQTRRI DQEILSAGFQ D LLVKEQTA ...String:
MAVEPITIAD LTEVKLDGKG ALDQLLQVTR LHLAKEHDAG RLKGQEYAAV LTGGITAVLQ NAVMFLLQKD EAANKAALVE AQIKLTEKQ GELLDKQIAQ ADKDAELIAA KVKLTLEQAK LPDSQIRSAG FQDLLVQEQT KVQTAQTRRI DQEILSAGFQ D LLVKEQTA KTKQDVLTAV QQTKVMEQQV LESTQKVLNM KQELLNLVAQ ECLLKAQFDL TKDQGLNTQE QTILVRQKVA SE RAQTIGA GVDADSVIGR QKELYKAQAD GFKRDAEQKA AKILIDTWNV RRTTDTGTQA NTTNRLDDAN VGRVVNMLMT GVG A

UniProtKB: N4 gp54-like protein

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Macromolecule #3: gp83 head-to-tail

MacromoleculeName: gp83 head-to-tail / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeP_DEV (virus)
Molecular weightTheoretical: 27.868934 KDa
SequenceString: MTIQLKQVID LLAEGELSNI KYVNIDTGAL VLERVPSLIR AINLGVLDLH KRFLLKEGML KIQLEEGRRL YPLRPAYQVG QKPKPGVPQ FITEGNKLGR QSILKIEKII GDNGVEYYLN DTWQPLNITT PEFDVLEISD EFYCHSSSKT LEVRYRRAPT P MKICVDNL ...String:
MTIQLKQVID LLAEGELSNI KYVNIDTGAL VLERVPSLIR AINLGVLDLH KRFLLKEGML KIQLEEGRRL YPLRPAYQVG QKPKPGVPQ FITEGNKLGR QSILKIEKII GDNGVEYYLN DTWQPLNITT PEFDVLEISD EFYCHSSSKT LEVRYRRAPT P MKICVDNL DSWGCIDIDL PYTHLQALLY FVASRCQTPI GFMENTAQEG FNFSQKYEAE CANLDAQNLR IDPVGNQDRF TR GGWV

UniProtKB: Uncharacterized protein

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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: 7
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9bgm

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 64223
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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