[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 YfdQ reveals a widespread family of bacteriophage-associated proteins with shell-like assemblies.
Journal, issue, pagesStructure, Year 2026
Publish dateApr 15, 2025
AuthorsDavi Gabriel Salustiano Merighi / Guilherme Camargo Pompeu / Gabriel Guarany de Araujo / Anacleto Silva de Souza / Germán Gustavo Sgro / Chuck Shaker Farah / Cristiane Rodrigues Guzzo /
PubMed AbstractBacteriophages are key players in microbial ecosystems with strong biotechnological potential, yet many phage-encoded proteins remain uncharacterized. We present the structure of the YfdQ complex ...Bacteriophages are key players in microbial ecosystems with strong biotechnological potential, yet many phage-encoded proteins remain uncharacterized. We present the structure of the YfdQ complex from the Xanthomonas citri ΦXacm4-11 phage, a conserved DUF2303 protein encoded by double-stranded DNA bacteriophages of the Caudoviricetes class. Using cryo-electron microscopy, we report that native YfdQ assembles into a shell-like structure with D18 symmetry forming a ∼1.1 MegaDalton complex, a hollow interior and a unique equatorial β strand stitching oligomerization interface that holds together the two hemispheres. YfdQ homologs are widely distributed among phages infecting diverse bacterial hosts, suggesting a conserved biological role. YfdQ are found in prophages and cryptic phages. Our results suggest that heterologous expression of YfdQ in X. citri and in Escherichia coli allows the obtention of structurally heterogeneous YfdQ complexes, suggesting that its proper assembly into the shell-like structure may depend on still unidentified viral factors.
External linksStructure / PubMed:42309054
MethodsEM (single particle)
Resolution3.9 Å
Structure data

70204
EMDB Unreleased entry

9o7m

EMDB-70204, PDB-9o7m:
Cryo-EM Structure of YfdQ Reveals a Widespread Novel Family of Bacteriophage-Associated Proteins with Shell-Like Assemblies
Method: EM (single particle) / Resolution: 3.9 Å

Source
  • caudoviricetes (bacterial and archaeal viruses with head-tail morphology)
KeywordsVIRAL PROTEIN / D18 symmetry / shell-like structure / DUF2303 / YfdQ

+
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