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- EMDB-74091: Asymmetric Tail Gating Complex of Pseudomonas Phage DEV -

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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: Pseudomonas aeruginosa DEV phage exploits the essential LptD outer membrane protein as receptor for adsorption
Authors: Noblecia JN / Bellis FN / Antichi C / Aminian S / Forti F / Falchi F / Bellis NF / Imperi F / Cingolani G / Briani F
History
DepositionNov 27, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74091.png

Downloads & links

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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 °

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Supplemental data

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Mask #1

Fileemd_74091_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_74091_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_74091_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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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

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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: 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

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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

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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

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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
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

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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)

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