[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

TitleArchitecture of the type IVa pilus machine.
Journal, issue, pagesScience, Vol. 351, Issue 6278, Page aad2001, Year 2016
Publish dateMar 11, 2016
AuthorsYi-Wei Chang / Lee A Rettberg / Anke Treuner-Lange / Janet Iwasa / Lotte Søgaard-Andersen / Grant J Jensen /
PubMed AbstractType IVa pili are filamentous cell surface structures observed in many bacteria. They pull cells forward by extending, adhering to surfaces, and then retracting. We used cryo-electron tomography of ...Type IVa pili are filamentous cell surface structures observed in many bacteria. They pull cells forward by extending, adhering to surfaces, and then retracting. We used cryo-electron tomography of intact Myxococcus xanthus cells to visualize type IVa pili and the protein machine that assembles and retracts them (the type IVa pilus machine, or T4PM) in situ, in both the piliated and nonpiliated states, at a resolution of 3 to 4 nanometers. We found that T4PM comprises an outer membrane pore, four interconnected ring structures in the periplasm and cytoplasm, a cytoplasmic disc and dome, and a periplasmic stem. By systematically imaging mutants lacking defined T4PM proteins or with individual proteins fused to tags, we mapped the locations of all 10 T4PM core components and the minor pilins, thereby providing insights into pilus assembly, structure, and function.
External linksScience / PubMed:26965631 / PubMed Central
MethodsEM (subtomogram averaging) / EM (tomography)
Structure data

EMDB-3247: Subtomogram average of a piliated type IVa pilus machine in wild-type Myxococcus xanthus cells
PDB-3jc8: Architectural model of the type IVa pilus machine in a piliated state
Method: EM (subtomogram averaging)

EMDB-3248:
Subtomogram average of a non-piliated type IVa pilus machine in wild-type Myxococcus xanthus cells
Method: EM (subtomogram averaging)

EMDB-3249:
Subtomogram average of a non-piliated type IVa pilus machine in Myxococcus xanthus cells with pilP knockout
Method: EM (subtomogram averaging)

EMDB-3250:
Subtomogram average of a piliated type IVa pilus machine in Myxococcus xanthus cells with PilP tagged with a superfolder GFP
Method: EM (subtomogram averaging)

EMDB-3251:
Subtomogram average of a non-piliated type IVa pilus machine in Myxococcus xanthus cells with PilP tagged with a superfolder GFP
Method: EM (subtomogram averaging)

EMDB-3252:
Subtomogram average of a piliated type IVa pilus machine in Myxococcus xanthus cells with tsaP knockout
Method: EM (subtomogram averaging)

EMDB-3253:
Subtomogram average of a non-piliated type IVa pilus machine in Myxococcus xanthus cells with tsaP knockout
Method: EM (subtomogram averaging)

EMDB-3254:
Subtomogram average of a piliated type IVa pilus machine in Myxococcus xanthus cells with PilO tagged with a superfolder GFP
Method: EM (subtomogram averaging)

EMDB-3255:
Subtomogram average of a non-piliated type IVa pilus machine in Myxococcus xanthus cells with PilO tagged with a superfolder GFP
Method: EM (subtomogram averaging)

EMDB-3256:
Subtomogram average of a non-piliated type IVa pilus machine in Myxococcus xanthus cells with pilC knockout
Method: EM (subtomogram averaging)

EMDB-3257:
Subtomogram average of a non-piliated type IVa pilus machine in Myxococcus xanthus cells with pilA knockout
Method: EM (subtomogram averaging)

EMDB-3258:
Subtomogram average of a non-piliated type IVa pilus machine in Myxococcus xanthus cells with pilV/pilW/fimU knockout
Method: EM (subtomogram averaging)

EMDB-3259:
Subtomogram average of a piliated type IVa pilus machine in Myxococcus xanthus cells with pilT knockout
Method: EM (subtomogram averaging)

EMDB-3260: Subtomogram average of a non-piliated type IVa pilus machine in Myxococcus xanthus cells with pilB knockout
PDB-3jc9: Architectural model of the type IVa pilus machine in a non-piliated state
Method: EM (subtomogram averaging)

EMDB-3261:
Subtomogram average of a non-piliated type IVa pilus machine in Myxococcus xanthus cells with pilB/pilT knockout
Method: EM (subtomogram averaging)

EMDB-3262:
Subtomogram average of a non-piliated type IVa pilus machine in Myxococcus xanthus cells with pilM knockout
Method: EM (subtomogram averaging)

EMDB-3263:
Subtomogram average of a piliated type IVa pilus machine in Myxococcus xanthus cells with pilQ 25-300 residues truncated
Method: EM (subtomogram averaging)

EMDB-3264:
Subtomogram average of a non-piliated type IVa pilus machine in Myxococcus xanthus cells with pilQ 25-300 residues truncated
Method: EM (subtomogram averaging)

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

Source
  • Myxococcus xanthus (bacteria)
  • myxococcus xanthus dk 1622 (bacteria)
KeywordsMOTOR PROTEIN / motor / pilus / ring / membrane channel

+
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