[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

TitleStructure of the T4 baseplate and its function in triggering sheath contraction.
Journal, issue, pagesNature, Vol. 533, Issue 7603, Page 346-352, Year 2016
Publish dateMay 19, 2016
AuthorsNicholas M I Taylor / Nikolai S Prokhorov / Ricardo C Guerrero-Ferreira / Mikhail M Shneider / Christopher Browning / Kenneth N Goldie / Henning Stahlberg / Petr G Leiman /
PubMed AbstractSeveral systems, including contractile tail bacteriophages, the type VI secretion system and R-type pyocins, use a multiprotein tubular apparatus to attach to and penetrate host cell membranes. This ...Several systems, including contractile tail bacteriophages, the type VI secretion system and R-type pyocins, use a multiprotein tubular apparatus to attach to and penetrate host cell membranes. This macromolecular machine resembles a stretched, coiled spring (or sheath) wound around a rigid tube with a spike-shaped protein at its tip. A baseplate structure, which is arguably the most complex part of this assembly, relays the contraction signal to the sheath. Here we present the atomic structure of the approximately 6-megadalton bacteriophage T4 baseplate in its pre- and post-host attachment states and explain the events that lead to sheath contraction in atomic detail. We establish the identity and function of a minimal set of components that is conserved in all contractile injection systems and show that the triggering mechanism is universally conserved.
External linksNature / PubMed:27193680
MethodsEM (single particle) / X-ray diffraction
Resolution2.47 - 6.77 Å
Structure data

EMDB-3374, PDB-5iv5:
Cryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex
Method: EM (single particle) / Resolution: 4.11 Å

EMDB-3392:
Cryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex: locally masked refinement of the inner baseplate
Method: EM (single particle) / Resolution: 3.83 Å

EMDB-3393:
Cryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex: locally masked refinement of the intermediate baseplate
Method: EM (single particle) / Resolution: 4.19 Å

EMDB-3394:
Cryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex: locally masked refinement of the upper peripheral baseplate
Method: EM (single particle) / Resolution: 4.55 Å

EMDB-3395:
Cryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex: locally masked refinement of the lower peripheral baseplate
Method: EM (single particle) / Resolution: 4.45 Å

EMDB-3396, PDB-5iv7:
Cryo-electron microscopy structure of the star-shaped, hubless post-attachment T4 baseplate
Method: EM (single particle) / Resolution: 6.77 Å

EMDB-3397:
Cryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex: locally masked refinement of the tail tube
Method: EM (single particle) / Resolution: 3.81 Å

PDB-5iw9:
Structure of bacteriophage T4 gp25, sheath polymerization initiator
Method: X-RAY DIFFRACTION / Resolution: 2.47 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-FE:
Unknown entry

ChemComp-HOH:
WATER

Source
  • enterobacteria phage t4 (virus)
KeywordsVIRAL PROTEIN / T4 / baseplate-tail tube complex / pre-attachment / bacteriophage / bacterial virus / hexagonal / membrane-piercing / cell attachment / infection / baseplate / post-attachment / star-shaped / hubless / contractile sheath / wedge / sheath polymerization

+
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