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- EMDB-49882: Pseudomonas phage Pa223 tail (C6 symmetry) -

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Basic information

Entry
Database: EMDB / ID: EMD-49882
TitlePseudomonas phage Pa223 tail (C6 symmetry)
Map data
Sample
  • Virus: Pseudomonas virus Pa223
    • Protein or peptide: Head-to-Tail adapter
    • Protein or peptide: Capsid and scaffold protein
KeywordsConstituent protein / Structural protein / Phage tail component / VIRUS
Function / homologySU10 adaptor protein / Constituent protein / Capsid and scaffold protein
Function and homology information
Biological speciesPseudomonas virus Pa223
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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 23, 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_49882.png

Downloads & links

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Map

FileDownload / File: emd_49882.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (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: 0.0212
Minimum - Maximum-0.108598456 - 0.19252501
Average (Standard dev.)-0.00011520956 (±0.0079797795)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Mask #1

Fileemd_49882_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49882_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_49882_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: Head-to-Tail adapter
    • Protein or peptide: Capsid and scaffold 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: Head-to-Tail adapter

MacromoleculeName: Head-to-Tail adapter / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa223
Molecular weightTheoretical: 24.10526 KDa
SequenceString: MATINNVTDL AIAAIQWSDR QDLTQELLML FIGNTTDRLN RLLRVRENEH FETLMAFGGG IEIPEHFVAL RSITGDSLIG GRTLQYITQ DIFTHYVNYN YQPQGVTYYT RLGNFWRVFP VVPDGAPFIV NYWTVLPELS LANPTTWALT KYPQIYLYGV L EQIYLYTM ...String:
MATINNVTDL AIAAIQWSDR QDLTQELLML FIGNTTDRLN RLLRVRENEH FETLMAFGGG IEIPEHFVAL RSITGDSLIG GRTLQYITQ DIFTHYVNYN YQPQGVTYYT RLGNFWRVFP VVPDGAPFIV NYWTVLPELS LANPTTWALT KYPQIYLYGV L EQIYLYTM DEARSQFWGQ KLERAVMELQ NEENAADFAS TRLAIKDIER

UniProtKB: Constituent protein

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Macromolecule #2: Capsid and scaffold protein

MacromoleculeName: Capsid and scaffold protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa223
Molecular weightTheoretical: 57.719672 KDa
SequenceString: MALERQEVKN PTGIVTDIAP ADLPLEKWSF GNNVRFKNGK AQKALGHTPI FDTAQAPILD MFPFIRNNIP YWLLCGEQRM YLADGTTVV DVSPGGHSAS VTSRWSSGSF NGVIFANNPS NYPYVLMPQN SGFIPMPNWP ANTFAKRMKS FKNFMIALNV T QNSVEMPQ ...String:
MALERQEVKN PTGIVTDIAP ADLPLEKWSF GNNVRFKNGK AQKALGHTPI FDTAQAPILD MFPFIRNNIP YWLLCGEQRM YLADGTTVV DVSPGGHSAS VTSRWSSGSF NGVIFANNPS NYPYVLMPQN SGFIPMPNWP ANTFAKRMKS FKNFMIALNV T QNSVEMPQ MVWWSTSADA GGIPVSWDPT DPTKDAGQNT LADTNGAIVD GVKLRDSFII YKEDSVYSMR YIGGLFIFQF QQ LFNDVGI LGPNCAIEFD GNHFVVGHGD VYVHNGVQKQ SVIDAQVRKF FFSDINPDNY QRTFVIADHV NTEMWVCYSS TRS EPGKHC DRAIIWNWKE NTWSIRDLPN VLSGAYGIID PKVSNLWDDD PNPWDTYTSV WGEGSYNPAK SSMIFSSFQD KKLF LFGNN STFSGQNFVS TLERSDIYLG DDRMMKTVSA IIPHITGNGT CNIWVGNAQV QGSGIRWKGP YPYRIGQDYK IDTKH VGRY IALKFDFSSE GDWYFNGYTI EMAPKAGMR

UniProtKB: Capsid and scaffold 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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46000
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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