[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleCryo-EM structure of ssDNA bacteriophage ΦCjT23 provides insight into early virus evolution.
Journal, issue, pagesNat Commun, Vol. 13, Issue 1, Page 7478, Year 2022
Publish dateDec 3, 2022
AuthorsNejc Kejzar / Elina Laanto / Ilona Rissanen / Vahid Abrishami / Muniyandi Selvaraj / Sylvain Moineau / Janne Ravantti / Lotta-Riina Sundberg / Juha T Huiskonen /
PubMed AbstractThe origin of viruses remains an open question. While lack of detectable sequence similarity hampers the analysis of distantly related viruses, structural biology investigations of conserved capsid ...The origin of viruses remains an open question. While lack of detectable sequence similarity hampers the analysis of distantly related viruses, structural biology investigations of conserved capsid protein structures facilitate the study of distant evolutionary relationships. Here we characterize the lipid-containing ssDNA temperate bacteriophage ΦCjT23, which infects Flavobacterium sp. (Bacteroidetes). We report ΦCjT23-like sequences in the genome of strains belonging to several Flavobacterium species. The virion structure determined by cryogenic electron microscopy reveals similarities to members of the viral kingdom Bamfordvirae that currently consists solely of dsDNA viruses with a major capsid protein composed of two upright β-sandwiches. The minimalistic structure of ΦCjT23 suggests that this phage serves as a model for the last common ancestor between ssDNA and dsDNA viruses in the Bamfordvirae. Both ΦCjT23 and the related phage FLiP infect Flavobacterium species found in several environments, suggesting that these types of viruses have a global distribution and a shared evolutionary origin. Detailed comparisons to related, more complex viruses not only expand our knowledge about this group of viruses but also provide a rare glimpse into early virus evolution.
External linksNat Commun / PubMed:36463224 / PubMed Central
MethodsEM (single particle)
Resolution3.2 - 5.3 Å
Structure data

15042

7zzz

EMDB-15042: Icosahedral reconstruction of bacteriophage phiCjT23 capsid
PDB-7zzz: Bacteriophage phiCjT23 capsid
Method: EM (single particle) / Resolution: 4.1 Å

15044

8a01

EMDB-15044: Localized reconstruction of bacteriophage phiCjT23 major capsid protein trimer type 1
PDB-8a01: Bacteriophage phiCjT23 major capsid protein trimer type 1
Method: EM (single particle) / Resolution: 3.2 Å

15045

8a02

EMDB-15045: Localized reconstruction of bacteriophage phiCjT23 major capsid protein trimer type 2
PDB-8a02: Bacteriophage phiCjT23 major capsid protein trimer type 2
Method: EM (single particle) / Resolution: 3.2 Å

15046

8a03

EMDB-15046: Localized reconstruction of bacteriophage phiCjT23 major capsid protein trimer type 3
PDB-8a03: Bacteriophage phiCjT23 major capsid protein trimer type 3
Method: EM (single particle) / Resolution: 3.2 Å

15047

8a04

EMDB-15047: Localized reconstruction of bacteriophage phiCjT23 major capsid protein trimer type 4
PDB-8a04: Bacteriophage phiCjT23 major capsid protein trimer type 4
Method: EM (single particle) / Resolution: 3.2 Å

15048

8a05

EMDB-15048, PDB-8a05:
Bacteriophage phiCjT23 spike protein penton domain
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-15049: Localized reconstruction of bacteriophage phiCjT23 spike
Method: EM (single particle) / Resolution: 5.3 Å

EMDB-15050: Composite map of bacteriophage phiCjT23 capsid calculated from localized reconstructions
Method: EM (single particle) / Resolution: 3.2 Å

15051

8a06

EMDB-15051: Localized reconstruction of flavobacterium infecting lipid-containing phage FLiP vertex
PDB-8a06: Flavobacterium infecting lipid-containing phage FLiP penton protein
Method: EM (single particle) / Resolution: 4.0 Å

Source
  • flavobacterium phage (virus)
  • unidentified (others)
  • flavobacterium phage flip (virus)
KeywordsVIRUS / bacteriophage / phiCjT23 / Flavobacterium / lipid-containing / phage / FLiP / penton protein

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more