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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 / Tail 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: 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 26, 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_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
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_74075_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_74075_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: Tail 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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