[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

TitleRemoval of type IV pili by a small RNA virus.
Journal, issue, pagesScience, Vol. 384, Issue 6691, Page eadl0635, Year 2024
Publish dateApr 5, 2024
AuthorsJirapat Thongchol / Zihao Yu / Laith Harb / Yiruo Lin / Matthias Koch / Matthew Theodore / Utkarsh Narsaria / Joshua Shaevitz / Zemer Gitai / Yinghao Wu / Junjie Zhang / Lanying Zeng /
PubMed AbstractThe retractile type IV pilus (T4P) is important for virulence of the opportunistic human pathogen . The single-stranded RNA (ssRNA) phage PP7 binds to T4P and is brought to the cell surface through ...The retractile type IV pilus (T4P) is important for virulence of the opportunistic human pathogen . The single-stranded RNA (ssRNA) phage PP7 binds to T4P and is brought to the cell surface through pilus retraction. Using fluorescence microscopy, we discovered that PP7 detaches T4P, which impairs cell motility and restricts the pathogen's virulence. Using cryo-electron microscopy, mutagenesis, optical trapping, and Langevin dynamics simulation, we resolved the structure of PP7, T4P, and the PP7/T4P complex and showed that T4P detachment is driven by the affinity between the phage maturation protein and its bound pilin, plus the pilus retraction force and speed, and pilus bending. Pilus detachment may be widespread among other ssRNA phages and their retractile pilus systems and offers new prospects for antibacterial prophylaxis and therapeutics.
External linksScience / PubMed:38574145
MethodsEM (single particle)
Resolution3.6 - 7.9 Å
Structure data

41625

8tum

EMDB-41625, PDB-8tum:
Type IV pilus from Pseudomonas PAO1 strain
Method: EM (single particle) / Resolution: 3.6 Å

41632

8tux

EMDB-41632: Asymmetric reconstruction of mature PP7 virions
PDB-8tux: Capsid of mature PP7 virion with 3'end region of PP7 genomic RNA
Method: EM (single particle) / Resolution: 3.9 Å

41633

8tuw

EMDB-41633, PDB-8tuw:
Type IV pilus from Pseudomonas PAO1 strain with PP7 Maturation protein
Method: EM (single particle) / Resolution: 7.9 Å

EMDB-41675: The original consensus map of PP7 binding to T4P from PAO1
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-41780: Composite map of PP7 binding to type IV pilus from PAO1
Method: EM (single particle) / Resolution: 3.9 Å

Source
  • Pseudomonas aeruginosa (bacteria)
  • pseudomonas aeruginosa pao1 (bacteria)
  • pseudomonas phage pp7 (virus)
KeywordsMEMBRANE PROTEIN / Type IV pilus / T4P / PAO1 / VIRAL PROTEIN / Maturation protein / PP7 / pepevirus

+
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