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- EMDB-29487: Pseudomonas phage E217 neck (portal, head-to-tail connector, coll... -

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Basic information

Entry
Database: EMDB / ID: EMD-29487
TitlePseudomonas phage E217 neck (portal, head-to-tail connector, collar and gateway proteins)
Map data
Sample
  • Virus: Pseudomonas phage vB_PaeM_E217 (virus)
    • Protein or peptide: E217 collar protein gp28
    • Protein or peptide: E217 gateway protein gp29
    • Protein or peptide: E217 head-to-tail connector protein gp27
    • Protein or peptide: E217 portal protein gp19
Keywordspseudomonas / phage / E217 / VIRUS
Function / homology
Function and homology information


Protein of unknown function DUF4054 / Inorganic pyrophosphatase domain / Protein of unknown function (DUF4054) / Inorganic Pyrophosphatase / Protein of unknown function DUF1073 / Anti-CBASS protein Acb1-like
Similarity search - Domain/homology
Phage protein / Inorganic pyrophosphatase domain-containing protein / Phage protein / Virion protein
Similarity search - Component
Biological speciesPseudomonas phage vB_PaeM_E217 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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 18, 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_29487.png

Downloads & links

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Map

FileDownload / File: emd_29487.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.12 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.026663095 - 0.04939805
Average (Standard dev.)0.00006355236 (±0.002784263)
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_29487_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_29487_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 phage vB_PaeM_E217

EntireName: Pseudomonas phage vB_PaeM_E217 (virus)
Components
  • Virus: Pseudomonas phage vB_PaeM_E217 (virus)
    • Protein or peptide: E217 collar protein gp28
    • Protein or peptide: E217 gateway protein gp29
    • Protein or peptide: E217 head-to-tail connector protein gp27
    • Protein or peptide: E217 portal protein gp19

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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: E217 collar protein gp28

MacromoleculeName: E217 collar protein gp28 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Molecular weightTheoretical: 14.234122 KDa
SequenceString:
IPGANLLRMA FGVIGTQIVR YRKFEQRVKN DQAQYVSMFG EPFDLAASVQ RVRRDQYAQF NLEFQRNYVM IFANFDMVDL DRNMAGDQF LWTGRVFQLE SQGSWFYQDG WGVCLAVDIG AAKA

UniProtKB: Virion protein

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Macromolecule #2: E217 gateway protein gp29

MacromoleculeName: E217 gateway protein gp29 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Molecular weightTheoretical: 21.057492 KDa
SequenceString:
MFDGELIAKL VVELNAAMTS AQEALQFPDF EVVQKAQPTQ QGTSTRPTIF FQKLFDIPRG WPATDWHLDN TARKYVEITR QHVETTFQI SSLHWQNPEI THVVTASDIA NYVRAYFQAR STIERVKELD FLILRVSQIS NEAFENDNHQ FEFHPSFDMV V TYNQYIRL YENAAYSADG VLIG

UniProtKB: Phage protein

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Macromolecule #3: E217 head-to-tail connector protein gp27

MacromoleculeName: E217 head-to-tail connector protein gp27 / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Molecular weightTheoretical: 16.885285 KDa
SequenceString:
MVIFDEHKFR TLFPEFADPA AYPDVRLQMY FDIACEFISD RDSPYRILNG KALEACLYLL TAHLLSLSTM QVQGAAGGGV TAGGTQGGF ITSATVGEVS VAKLAPPAKN GWQWWLSGTP YGQELWALLS VKAVGGFYIG GLPERRGFRK VGGTFW

UniProtKB: Phage protein

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Macromolecule #4: E217 portal protein gp19

MacromoleculeName: E217 portal protein gp19 / type: protein_or_peptide / ID: 4 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Molecular weightTheoretical: 48.635984 KDa
SequenceString: PTMLQDWYNS QGFIGYQACA IISQHWLVDK ACSMSGEDAA RNGWELKSDG RKLSDEQSAL IARRDMEFRV KDNLVELNRF KNVFGVRIA LFVVESDDPD YYEKPFNPDG VTPGSYKGIS QIDPYWAMPQ LTAGSTADPS SEHFYEPDFW IISGKKYHRS H LVVVRGPQ ...String:
PTMLQDWYNS QGFIGYQACA IISQHWLVDK ACSMSGEDAA RNGWELKSDG RKLSDEQSAL IARRDMEFRV KDNLVELNRF KNVFGVRIA LFVVESDDPD YYEKPFNPDG VTPGSYKGIS QIDPYWAMPQ LTAGSTADPS SEHFYEPDFW IISGKKYHRS H LVVVRGPQ PPDILKPTYI FGGIPLTQRI YERVYAAERT ANEAPLLAMS KRTSTIHVDV EKAIANEEAF NARLAFWIAN RD NHGVKVL GIDEGMEQFD TNLADFDSII MNQYQLVAAI AKTPATKLLG TSPKGFNATG EHETISYHEE LESIQEHIFD PLL ERHYLL LAKSEEIDVQ LEIVWNPVDS TSSQQQAELN NKKAATDEIY INSGVVSPDE VRERLRDDPR SGYNRLTDDQ AETE PGMSP ENLAEFEKAG AQSAKAKGEA ERAEAQAG

UniProtKB: Inorganic pyrophosphatase domain-containing 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 9000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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