[English] 日本語
Yorodumi
- EMDB-74091: Asymmetric Tail Gating Complex of Pseudomonas Phage DEV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-74091
TitleAsymmetric Tail Gating Complex of Pseudomonas Phage DEV
Map data
Sample
  • Virus: Pseudomonas phage vB_PaeP_DEV (virus)
    • Protein or peptide: gp75 tail tube
    • Protein or peptide: N4 gp53-like protein
    • Protein or peptide: Tip attachment protein J central straight fiber domain-containing protein
Keywordsvirus / bacteriophage / receptor-binding protein / VIRAL 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.5 Å
AuthorsBellis NF / Cingolani G
Funding support United States, 2 items
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, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_74091.png

Downloads & links

-
Map

FileDownload / File: emd_74091.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 640 pix.
= 764.16 Å		1.19 Å/pix.
x 640 pix.
= 764.16 Å		1.19 Å/pix.
x 640 pix.
= 764.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.194 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0176
Minimum - Maximum-0.10947166 - 0.308167
Average (Standard dev.)-0.0012528097 (±0.008796951)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 764.16003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_74091_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_74091_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_74091_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Pseudomonas phage vB_PaeP_DEV

EntireName: Pseudomonas phage vB_PaeP_DEV (virus)
Components
  • Virus: Pseudomonas phage vB_PaeP_DEV (virus)
    • Protein or peptide: gp75 tail tube
    • Protein or peptide: N4 gp53-like protein
    • Protein or peptide: Tip attachment protein J central straight fiber domain-containing protein

-
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

-
Macromolecule #1: gp75 tail tube

MacromoleculeName: gp75 tail tube / type: protein_or_peptide / ID: 1 / 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

-
Macromolecule #2: N4 gp53-like protein

MacromoleculeName: N4 gp53-like protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeP_DEV (virus)
Molecular weightTheoretical: 82.267039 KDa
SequenceString: MGLFSSKKKT VVNTTVQRVF DDAHIPDSPR TGVIQGITHE TGIVENILEK LSDSIGVRAN TAYLWAQRNN YYWGLPESKV VNGVDARTV VVQTIARSEG TITTYYNQFG PLNSLHWGFT ELVRLYQYNP LTNELPGLST TKGSKVYLFD MIPVFQTDTV A WADETANK ...String:
MGLFSSKKKT VVNTTVQRVF DDAHIPDSPR TGVIQGITHE TGIVENILEK LSDSIGVRAN TAYLWAQRNN YYWGLPESKV VNGVDARTV VVQTIARSEG TITTYYNQFG PLNSLHWGFT ELVRLYQYNP LTNELPGLST TKGSKVYLFD MIPVFQTDTV A WADETANK GMLQDFGFSP KSGYTPSRPY NTIGGMGQFA GWSPYRTDNS FGEDYVLLTY EWKDAQGVIK QETIRMIMNL DL SLDYHQV RFRRQNGTQG FFTYQDGKGT YPLIDGVFNL DYTKQGTYYP WMYCRFNKMN VKDIPGNAYK DVKEVAKISG IGI DELIDG VHADPDIGDV AQVVLFYGVP PGATNQDQLT YIFEYLLLLH SEALAQIQKA ENLQGKLGDY SNTADQMITM RDKY FKMDF SFSGITVNRK SGKVGPIGFI NVKSGMADKS SGQIKTQQPA YTYTRQAMDS MYDEVIIYNP AMHYQITSKK GHVAQ LGQP ELLIPVDRVV LSQLGLRAQE QLLCRSLHMA INTQVQIKTP WYASGFFKVI LIVVAVAVTI FTAGSAWGTI VAAASL GVA ALTMVIVQMI VTTLAVSYGV KLFVRAVGPE LGILAAVAAL AVGAYGMSNN ATWSENLMAV SHGIAKESQT MEQAGLM DT LKELERNQTY YADQLQSLED QRRELGLVQF QALQGEDFVN RPLTILGEST DDFFSRTVHA GNIGAASFQL TEYFVDAK L QLPSINETIE EINNGLSVQ

UniProtKB: N4 gp53-like protein

-
Macromolecule #3: Tip attachment protein J central straight fiber domain-containing...

MacromoleculeName: Tip attachment protein J central straight fiber domain-containing protein
type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeP_DEV (virus)
Molecular weightTheoretical: 46.398672 KDa
SequenceString: MVDTCNINGV CGTGDWNGPK PGDPNMNDLL LKATPAFGGI DIEFTWPTTN PGAVGTTRLF RSTDANFAGA TIRAFVNGNF YFDKTDPGS KVDQRYYYWI QLVSINGTDG DIIGPATATA RPLIEQMIEQ LTGEIDNGLL SQELRQEIAQ IELNKLGITQ E EIERAKND ...String:
MVDTCNINGV CGTGDWNGPK PGDPNMNDLL LKATPAFGGI DIEFTWPTTN PGAVGTTRLF RSTDANFAGA TIRAFVNGNF YFDKTDPGS KVDQRYYYWI QLVSINGTDG DIIGPATATA RPLIEQMIEQ LTGEIDNGLL SQELRQEIAQ IELNKLGITQ E EIERAKND DALGVRLTQI DAKMDQNTAI LQEEVRARVT ADSSLVQTVN TMYADFNGNI AAIQQENTAL ATKVNALASS VT TINATVN GDSASGKVGL VAEVQTLDGK VTQIGARWTA TVDVNGLVGG FGVYNDGRTV EAGFNVDRFW IGRPGTPKNP GSY PFIIDN NIVYIKEAAI QKLTFDKLRA QDGSFIVQNG KIQADYIEAK DIVVNNIQSD NYQPGVQGWA FRPNGIMEIN GTAG TGRMT INNATIKVFD QAGKLRVHIG NLQA

UniProtKB: Tip attachment protein J central straight fiber domain-containing protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 8241
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more