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- EMDB-29481: Pseudomonas phage E217 extended sheath and tail tube -

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Basic information

Entry
Database: EMDB / ID: EMD-29481
TitlePseudomonas phage E217 extended sheath and tail tube
Map data
Sample
  • Virus: Pseudomonas phage vB_PaeM_E217 (virus)
    • Protein or peptide: Sheath protein gp31
    • Protein or peptide: Tail fiber protein gp32
KeywordsPseudomonas / phage / E217 / VIRUS
Function / homologyProtein of unknown function DUF3383 / Protein of unknown function (DUF3383) / Tail fiber protein / Tail sheath protein
Function and homology information
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-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29481.png

Downloads & links

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Map

FileDownload / File: emd_29481.map.gz / Format: CCP4 / Size: 103 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-0.022184063 - 0.067347996
Average (Standard dev.)0.00067497004 (±0.006061163)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_29481_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_29481_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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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: Sheath protein gp31
    • Protein or peptide: Tail fiber protein gp32

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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: No / Virus empty: No

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Macromolecule #1: Sheath protein gp31

MacromoleculeName: Sheath protein gp31 / type: protein_or_peptide / ID: 1 / Details: Extended state / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Molecular weightTheoretical: 53.69475 KDa
SequenceString: MISQSRYIRI ISGVGAAAPV AGRKLILRVM TTNNVIPPGI VIEFDNANAV LSYFGAQSEE YQRAAAYFKF ISKSVNSPSS ISFARWVNT AIAPMVVGDN LPKTIADFAG FSAGVLTIMV GAAEQNITAI DTSAATSMDN VASIIQTEIR KNADPQLAQA T VTWNQNTN ...String:
MISQSRYIRI ISGVGAAAPV AGRKLILRVM TTNNVIPPGI VIEFDNANAV LSYFGAQSEE YQRAAAYFKF ISKSVNSPSS ISFARWVNT AIAPMVVGDN LPKTIADFAG FSAGVLTIMV GAAEQNITAI DTSAATSMDN VASIIQTEIR KNADPQLAQA T VTWNQNTN QFTLVGATIG TGVLAVAKSA DPQDMSTALG WSTSNVVNVA GQSADLPDAA VAKSTNVSNN FGSFLFAGAP LD NDQIKAV SAWNAAQNNQ FIYTVATSLA NLGTLFTLVN GNAGTALNVL SATAANDFVE QCPSEILAAT NYDEPGASQN YMY YQFPGR NITVSDDTVA NTVDKSRGNY IGVTQANGQQ LAFYQRGILC GGPTDAVDMN VYANEIWLKS AIAQALLDLF LNVN AVPAS STGEAMTLAV LQPVLDKATA NGTFTYGKEI SAVQQQYITQ VTGDRRAWRQ VQTLGYWINI TFSSYTNSNT GLTEW KANY TLIYSKGDAI RFVEGSDVMI

UniProtKB: Tail sheath protein

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Macromolecule #2: Tail fiber protein gp32

MacromoleculeName: Tail fiber protein gp32 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Molecular weightTheoretical: 15.174168 KDa
SequenceString:
FGSICAFTAS RTFPNGFTVT EEFADADPID SPPFAAADTG AGLNGDMVVW NRANILEVVV NVIPNTEGER NLAVLLDANR TGKDKSGAR DVVGLVVAMP DGSKITCTNG TPIDGVLINA VASVGRLKTK PYRFRFEKVI KAGTS

UniProtKB: Tail fiber 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 / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: OTHER / Average electron dose: 1.25 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10000
FSC plot (resolution estimation)

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