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- EMDB-49909: Pseudomonas phage Pa223 periplasmic tunnel (pre-ejection, dodecam... -

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Basic information

Entry
Database: EMDB / ID: EMD-49909
TitlePseudomonas phage Pa223 periplasmic tunnel (pre-ejection, dodecameric assembly)
Map data
Sample
  • Virus: Pseudomonas virus Pa223
    • Protein or peptide: Pseudomonas phage Pa223 Ejection protein, periplasmic tunnel
KeywordsConstituent protein / Structural protein / Phage tail component / VIRUS
Function / homologyParticle protein
Function and homology information
Biological speciesPseudomonas virus Pa223
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsHou CFD / Cingolani G / Lokareddy KR
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM140733 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100888 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)OD024978 United States
CitationJournal: To Be Published
Title: High-resolution cryo-EM analysis of the therapeutic Pseudomonas phage Pa223
Authors: Hou CFD / Lokareddy KR / Cingolani G
History
DepositionMar 25, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49909.png

Downloads & links

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Map

FileDownload / File: emd_49909.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 512 pix.
= 484.352 Å		0.95 Å/pix.
x 512 pix.
= 484.352 Å		0.95 Å/pix.
x 512 pix.
= 484.352 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.946 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.024282198 - 0.055822283
Average (Standard dev.)0.0020625507 (±0.0034514)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 484.352 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49909_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49909_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 : Pseudomonas virus Pa223

EntireName: Pseudomonas virus Pa223
Components
  • Virus: Pseudomonas virus Pa223
    • Protein or peptide: Pseudomonas phage Pa223 Ejection protein, periplasmic tunnel

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Supramolecule #1: Pseudomonas virus Pa223

SupramoleculeName: Pseudomonas virus Pa223 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2590840 / Sci species name: Pseudomonas virus Pa223 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Macromolecule #1: Pseudomonas phage Pa223 Ejection protein, periplasmic tunnel

MacromoleculeName: Pseudomonas phage Pa223 Ejection protein, periplasmic tunnel
type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa223
Molecular weightTheoretical: 53.610738 KDa
SequenceString: MASMAYEGSP IRPSILRAAQ NELDMARIAR NKLPLAVEGS GLPDRVRRAA QAALENPDRW SRAAQEVAPA AEATGRGALG RIAGILGGP VSVGIQAAVT PGELGDAERT RAEEMAQASQ AVENMGPEVA QEANQWAQGV GQRAAQNATG GPTGAELLSY G VTPNQPSI ...String:
MASMAYEGSP IRPSILRAAQ NELDMARIAR NKLPLAVEGS GLPDRVRRAA QAALENPDRW SRAAQEVAPA AEATGRGALG RIAGILGGP VSVGIQAAVT PGELGDAERT RAEEMAQASQ AVENMGPEVA QEANQWAQGV GQRAAQNATG GPTGAELLSY G VTPNQPSI EPEITPEVAS EAGAAVADEE EANRQVIQQG AAEGLRTGAV SRPEMAQAVV EADAQREGVE LKPQELKNRV NE ELTQMRT MDNDDLSRYV SYALIGTGLL ASAIDKTGKA GDMFAASYER QLDRNLQAGI NQQKMAAAAA DRQIKEKDLE RKV AKDAAD VRLGEGNLEV KKGTLEETSR KNTGLLDRWA EEAARGRANL ALTQRGQDMA NQRAQLQAET TRRGQDMSQE NAQL SSAVR LKTAKISAQA RQAAAKAARG EPVTTKDALG ILSEVSGSQA LGGKKLGKTA QQAIAQTLRN EMRANPGANP IGIIQ REAA KLQPTGNWFF GGDLDYPAPT R

UniProtKB: Particle 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 62000
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: RANDOM CONICAL TILT / Random conical tilt - Number images: 46000 / Random conical tilt - Tilt angle: 15 degrees
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46120
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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