[English] 日本語
Yorodumi
- EMDB-29406: Pseudomonas phage E217 5-fold vertex (capsid and decorating proteins) -

+
Open data


ID or keywords:

Loading...

-
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 / homology: / Structural cement protein (E217 gp24/Pam3 gp6) / 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-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_29406.png

Downloads & links

-
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
Contrast
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)

Slices (2/3)

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 °

-
Supplemental data

-
Half map: #1

Fileemd_29406_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_29406_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
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

+
Image processing

Particle selectionNumber selected: 9300
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more