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- EMDB-29406: Pseudomonas phage E217 5-fold vertex (capsid and decorating proteins) -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-29406
TitlePseudomonas phage E217 5-fold vertex (capsid and decorating proteins)
Map data
Sample
  • Virus: Pseudomonas phage vB_PaeM_E217 (virus)
    • Protein or peptide: Major structural protein
    • Protein or peptide: Structural protein gp24
KeywordsPseudomonas / phage / E217 / VIRUS / capsid / decorating proteins
Function / homologyStructural protein gp24 / Capsid and scaffold protein / Virion protein
Function and homology information
Biological speciesPseudomonas phage vB_PaeM_E217 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.96 Å
AuthorsLi F / Cingolani G / Hou C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)GM140733 United States
CitationJournal: Nat Commun / Year: 2023
Title: High-resolution cryo-EM structure of the Pseudomonas bacteriophage E217.
Authors: Fenglin Li / Chun-Feng David Hou / Ravi K Lokareddy / Ruoyu Yang / Francesca Forti / Federica Briani / Gino Cingolani /
Abstract: E217 is a Pseudomonas phage used in an experimental cocktail to eradicate cystic fibrosis-associated Pseudomonas aeruginosa. Here, we describe the structure of the whole E217 virion before and after ...E217 is a Pseudomonas phage used in an experimental cocktail to eradicate cystic fibrosis-associated Pseudomonas aeruginosa. Here, we describe the structure of the whole E217 virion before and after DNA ejection at 3.1 Å and 4.5 Å resolution, respectively, determined using cryogenic electron microscopy (cryo-EM). We identify and build de novo structures for 19 unique E217 gene products, resolve the tail genome-ejection machine in both extended and contracted states, and decipher the complete architecture of the baseplate formed by 66 polypeptide chains. We also determine that E217 recognizes the host O-antigen as a receptor, and we resolve the N-terminal portion of the O-antigen-binding tail fiber. We propose that E217 design principles presented in this paper are conserved across PB1-like Myoviridae phages of the Pbunavirus genus that encode a ~1.4 MDa baseplate, dramatically smaller than the coliphage T4.
History
DepositionJan 8, 2023-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29406.png

Downloads & links

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Map

FileDownload / File: emd_29406.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 512 pix.
= 573.44 Å		1.12 Å/pix.
x 512 pix.
= 573.44 Å		1.12 Å/pix.
x 512 pix.
= 573.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.0197
Minimum - Maximum-0.025847679 - 0.061050992
Average (Standard dev.)-0.0002547665 (±0.0052388636)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 573.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_29406_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_29406_half_map_2.map
Projections & Slices
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Sample components

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Entire : Pseudomonas phage vB_PaeM_E217

EntireName: Pseudomonas phage vB_PaeM_E217 (virus)
Components
  • Virus: Pseudomonas phage vB_PaeM_E217 (virus)
    • Protein or peptide: Major structural protein
    • Protein or peptide: Structural protein gp24

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Supramolecule #1: Pseudomonas phage vB_PaeM_E217

SupramoleculeName: Pseudomonas phage vB_PaeM_E217 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2034346 / Sci species name: Pseudomonas phage vB_PaeM_E217 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes

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Macromolecule #1: Major structural protein

MacromoleculeName: Major structural protein / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Molecular weightTheoretical: 34.735047 KDa
SequenceString: NFTAPVTTPS IPTPIQFLQT WLPGFVKVMT AARKIDEIIG IDTVGSWEDQ EIVQGIVEPA GTAVEYGDHT NIPLTSWNAN FERRTIVRG ELGMMVGTLE EGRASAIRLN SAETKRQQAA IGLETFRNAI GFYGWQSGLG NRTYGFLNDP NLPAFQTPPS Q GWSTADWA ...String:
NFTAPVTTPS IPTPIQFLQT WLPGFVKVMT AARKIDEIIG IDTVGSWEDQ EIVQGIVEPA GTAVEYGDHT NIPLTSWNAN FERRTIVRG ELGMMVGTLE EGRASAIRLN SAETKRQQAA IGLETFRNAI GFYGWQSGLG NRTYGFLNDP NLPAFQTPPS Q GWSTADWA GIIGDIREAV RQLRIQSQDQ IDPKAEKITL ALATSKVDYL SVTTPYGISV SDWIEQTYPK MRIVSAPELS GV QMKNQEP EDALVLFVED VNAAVDGSTD GGSVFSQLVQ SKFITLGVEK RAKSYVEDFS NGTAGALCKR PWAVVRYLGI

UniProtKB: Capsid and scaffold protein

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Macromolecule #2: Structural protein gp24

MacromoleculeName: Structural protein gp24 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Molecular weightTheoretical: 21.610312 KDa
SequenceString: MFQKQVYRQY TPGFPGDLIE DGPKRARPGR IMSLSAVNPA ATATGPNRAS RAFGYAGDVS ALGEGQPKTI AARASEVVIG GANFFGVLG HPKHYALFGS AGDSLAPSYD LPDGAEGEFF DMATGLVVEI FNGAAAALDL DYGDLVAYVP NNLATADDAL G LPAGALVG ...String:
MFQKQVYRQY TPGFPGDLIE DGPKRARPGR IMSLSAVNPA ATATGPNRAS RAFGYAGDVS ALGEGQPKTI AARASEVVIG GANFFGVLG HPKHYALFGS AGDSLAPSYD LPDGAEGEFF DMATGLVVEI FNGAAAALDL DYGDLVAYVP NNLATADDAL G LPAGALVG FKTGSMPTGL VQIPNARIVN AISLPAQSAG NLVAGVTIVQ LTQ

UniProtKB: Virion 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 9300
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9300
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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