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- EMDB-49910: Pseudomonas phage Pa223 tail needle -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-49910
TitlePseudomonas phage Pa223 tail needle
Map data
Sample
  • Virus: Pseudomonas virus Pa223
    • Protein or peptide: Constituent protein
KeywordsConstituent protein / Structural protein / Phage tail component / VIRUS
Function / homologyConstituent protein
Function and homology information
Biological speciesPseudomonas virus Pa223
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 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_49910.png

Downloads & links

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Map

FileDownload / File: emd_49910.map.gz / Format: CCP4 / Size: 343 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 448 pix.
= 423.808 Å		0.95 Å/pix.
x 448 pix.
= 423.808 Å		0.95 Å/pix.
x 448 pix.
= 423.808 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-0.025184453 - 0.04682913
Average (Standard dev.)-0.00058537617 (±0.0030240344)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 423.80798 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_49910_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49910_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: Constituent protein

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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: Constituent protein

MacromoleculeName: Constituent protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa223
Molecular weightTheoretical: 25.164588 KDa
SequenceString: MSQKYSPSIP PQEEEELLPF LNEEFVRVGQ TLNDLADGYW GVSMEPPKKL KPGTVKYFAP GVVGPVSGIY HYDLDNQWRL AGTKPKDLP GDFILFTPQN NHQPMGTCAY RMNTAKDEVW ITMLMSGGNY TNGATVLDLP QAYWPPAELF IPAYSSIIPA Q STITYPPP ...String:
MSQKYSPSIP PQEEEELLPF LNEEFVRVGQ TLNDLADGYW GVSMEPPKKL KPGTVKYFAP GVVGPVSGIY HYDLDNQWRL AGTKPKDLP GDFILFTPQN NHQPMGTCAY RMNTAKDEVW ITMLMSGGNY TNGATVLDLP QAYWPPAELF IPAYSSIIPA Q STITYPPP SDPNAPPLDQ VFDVLNRATI QTGVVNQAMF KITANGRVLI QGIPQGAVFG GTFTFPLVVT P

UniProtKB: Constituent 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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14000
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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