[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

TitleIn situ structures of the portal-neck-tail complex of bacteriophage T4 inform a viral genome positioning mechanism.
Journal, issue, pagesNat Commun, Vol. 17, Year 2026
Publish dateDec 17, 2024
AuthorsAndrei Fokine / Jingen Zhu / Thomas Klose / Frank Vago / Charles-Adrien Arnaud / Zhiqing Wang / Baldeep Khare / Michael G Rossmann / Zhenguo Chen / Lei Sun / Qianglin Fang / Richard J Kuhn / Venigalla B Rao /
PubMed AbstractThe post-genome packaging mechanisms that govern the assembly of an infectious virion are poorly understood in bacteriophages and other viruses. Here, our near-atomic resolution cryo-EM structural ...The post-genome packaging mechanisms that govern the assembly of an infectious virion are poorly understood in bacteriophages and other viruses. Here, our near-atomic resolution cryo-EM structural analyses uncovered an assembly- and conformation-driven genome positioning mechanism in the tailed bacteriophage T4. We show that following headful packaging, which generates a pressurized head, a global conformational change occurs in the portal structure, probably triggering packaging termination and ejection of the packaging motor. Our high-resolution structures of the neck of the virion further show that the neck undergoes conformational changes upon docking of a pre-assembled tail onto the sealed neck, which then opens a genome-gate. Driven by the pressure of the packaged DNA, the genome travels through open neck channels, binds and compresses the resident tape-measure protein, and halts at the bottom of the second topmost disk of the tail tube. Pressure-suspended within the virion's innermost tunnel and secured by a baseplate plug, the genome remains poised to flow through the tunnel into a host cell upon receiving the host receptor recognition signal.
External linksNat Commun / PubMed:41720772 / PubMed Central
MethodsEM (single particle)
Resolution3.8 Å
Structure data

48324

9mkb

EMDB-48324, PDB-9mkb:
Structure of the bacteriophage T4 portal-neck-tail complex
Method: EM (single particle) / Resolution: 3.8 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • escherichia phage t4 (virus)
KeywordsVIRAL PROTEIN / bacteriophage T4 / portal vertex / phage neck / phage tail / contractile sheath / tail tube / baseplate / VIRUS

+
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