[English] 日本語
Yorodumi
- PDB-8fvh: Pseudomonas phage E217 neck (portal, head-to-tail connector, coll... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fvh
TitlePseudomonas phage E217 neck (portal, head-to-tail connector, collar and gateway proteins)
Components
  • E217 collar protein gp28
  • E217 gateway protein gp29
  • E217 head-to-tail connector protein gp27
  • E217 portal protein gp19
KeywordsVIRUS / pseudomonas / phage / E217
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLi, F. / Cingolani, G. / Hou, C.
Funding support United States, 1items
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, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: E217 collar protein gp28
A: E217 collar protein gp28
B: E217 collar protein gp28
D: E217 collar protein gp28
E: E217 collar protein gp28
F: E217 collar protein gp28
M: E217 gateway protein gp29
P: E217 gateway protein gp29
S: E217 gateway protein gp29
V: E217 gateway protein gp29
Y: E217 gateway protein gp29
b: E217 gateway protein gp29
N: E217 head-to-tail connector protein gp27
Q: E217 head-to-tail connector protein gp27
T: E217 head-to-tail connector protein gp27
W: E217 head-to-tail connector protein gp27
Z: E217 head-to-tail connector protein gp27
c: E217 head-to-tail connector protein gp27
G: E217 head-to-tail connector protein gp27
H: E217 head-to-tail connector protein gp27
I: E217 head-to-tail connector protein gp27
J: E217 head-to-tail connector protein gp27
K: E217 head-to-tail connector protein gp27
L: E217 head-to-tail connector protein gp27
O: E217 portal protein gp19
R: E217 portal protein gp19
U: E217 portal protein gp19
X: E217 portal protein gp19
a: E217 portal protein gp19
d: E217 portal protein gp19
e: E217 portal protein gp19
f: E217 portal protein gp19
g: E217 portal protein gp19
h: E217 portal protein gp19
i: E217 portal protein gp19
j: E217 portal protein gp19


Theoretical massNumber of molelcules
Total (without water)998,00536
Polymers998,00536
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
E217 collar protein gp28


Mass: 14234.122 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8I4A6
#2: Protein
E217 gateway protein gp29


Mass: 21057.492 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8HWZ4
#3: Protein
E217 head-to-tail connector protein gp27


Mass: 16885.285 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8HNR2
#4: Protein
E217 portal protein gp19


Mass: 48635.984 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8HWX3

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Pseudomonas phage vB_PaeM_E217 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Details of virusEmpty: YES / Enveloped: YES / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal magnification: 81000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
2RELION3.1.2image acquisition
4RELION3.1.2CTF correction
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 9300
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00372114
ELECTRON MICROSCOPYf_angle_d0.55997848
ELECTRON MICROSCOPYf_dihedral_angle_d4.6059660
ELECTRON MICROSCOPYf_chiral_restr0.04310404
ELECTRON MICROSCOPYf_plane_restr0.00412912

+
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