[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

TitleThe Legionella pneumophila Dot/Icm Type IV Secretion System is Structurally and Functionally Resilient in Absence of Species-specific Proteins Dis2 and Dis3.
Journal, issue, pagesJ Mol Biol, Vol. 437, Issue 19, Page 169310, Year 2025
Publish dateJun 26, 2025
AuthorsJacquelyn R Roberts / Arwen E Frick-Cheng / Henry J Styron / Clarissa L Durie / Louise Chang / Melanie D Ohi /
PubMed AbstractLegionella pneumophila is a pathogenic Gram-negative bacterium that causes Legionnaires' disease. The main virulence factor of L. pneumophila is the Dot/Icm Type IV Secretion System (T4SS), which ...Legionella pneumophila is a pathogenic Gram-negative bacterium that causes Legionnaires' disease. The main virulence factor of L. pneumophila is the Dot/Icm Type IV Secretion System (T4SS), which translocates effector proteins into the cytoplasm of the host cell, allowing the bacterium to establish a replicative niche. The outer membrane core complex (OMCC), the T4SS machinery localized between the inner and outer membranes, is composed of at least nine proteins organized into various sub-complexes that include the dome, outer membrane cap (OMC), periplasmic ring (PR), and stalk. In this study we describe how two uncharacterized Dot/Icm T4SS components, Dis2 and Dis3, contribute to the structure of the T4SS, the ability of the T4SS to translocate effectors, and the pathogenicity of L. pneumophila. Using cryo-electron microscopy we show that OMCCs purified from a Δdis2 strain are only missing the density for Dis2, while OMCCs purified from the Δdis3 strain lack densities for Dis3 and DotF in the OMC. Despite missing these proteins, the OMC and PR of both mutant OMCCs remain structurally stable. Strains lacking dis2 and or dis3 efficiently replicate in human macrophages; however, they have subtle differences in translocation efficiency for four tested substrates. Combined these data indicate that Dis2 or Dis3 are not required for the stability or global organization of the OMCC, but each protein may contribute to the efficient translocation of specific effectors.
External linksJ Mol Biol / PubMed:40581092
MethodsEM (single particle)
Resolution3.6 - 6.3 Å
Structure data

EMDB-70321: Cryo-EM Structure of the Legionella pneumophila delta dis3 OMC
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-70322: Cryo-EM Structure of the Legionella pneumophila delta dis3 PR
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-70323: Cryo-EM Structure of the Legionella pneumophila delta dis2 OMC
Method: EM (single particle) / Resolution: 6.1 Å

EMDB-70324: Cryo-EM Structure of the Legionella pneumophila delta dis2 PR
Method: EM (single particle) / Resolution: 6.3 Å

Source
  • Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)

+
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