[English] 日本語
EMN Papers
- Database of articles cited by 3DEM data entries -

+
Search query

Keywords
Author
Journal
IF

-
Structure paper

TitleFine structure and assembly pattern of a minimal myophage Pam3.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 120, Issue 4, Page e2213727120, Year 2023
Publish dateJan 24, 2023
AuthorsFeng Yang / Yong-Liang Jiang / Jun-Tao Zhang / Jie Zhu / Kang Du / Rong-Cheng Yu / Zi-Lu Wei / Wen-Wen Kong / Ning Cui / Wei-Fang Li / Yuxing Chen / Qiong Li / Cong-Zhao Zhou /
PubMed AbstractThe myophage possesses a contractile tail that penetrates its host cell envelope. Except for investigations on the bacteriophage T4 with a rather complicated structure, the assembly pattern and tail ...The myophage possesses a contractile tail that penetrates its host cell envelope. Except for investigations on the bacteriophage T4 with a rather complicated structure, the assembly pattern and tail contraction mechanism of myophage remain largely unknown. Here, we present the fine structure of a freshwater cyanophage Pam3, which has an icosahedral capsid of ~680 Å in diameter, connected via a three-section neck to an 840-Å-long contractile tail, ending with a three-module baseplate composed of only six protein components. This simplified baseplate consists of a central hub-spike surrounded by six wedge heterotriplexes, to which twelve tail fibers are covalently attached via disulfide bonds in alternating upward and downward configurations. In vitro reduction assays revealed a putative redox-dependent mechanism of baseplate assembly and tail sheath contraction. These findings establish a minimal myophage that might become a user-friendly chassis phage in synthetic biology.
External linksProc Natl Acad Sci U S A / PubMed:36656854 / PubMed Central
MethodsEM (single particle) / EM (helical sym.)
Resolution3.0 - 3.96 Å
Structure data

EMDB-33799, PDB-7yfw:
Cyanophage Pam3 fiber
Method: EM (single particle) / Resolution: 3.96 Å

EMDB-33802, PDB-7yfz:
Cyanophage Pam3 baseplate proteins
Method: EM (single particle) / Resolution: 3.19 Å

EMDB-34678, PDB-8hdr:
Cyanophage Pam3 neck
Method: EM (single particle) / Resolution: 3.66 Å

EMDB-34679, PDB-8hds:
Cyanophage Pam3 portal-adaptor
Method: EM (single particle) / Resolution: 3.57 Å

EMDB-34680, PDB-8hdt:
Cyanophage Pam3 capsid asymmetric unit
Method: EM (single particle) / Resolution: 3.17 Å

EMDB-34681, PDB-8hdw:
Cyanophage Pam3 Sheath-tube
Method: EM (helical sym.) / Resolution: 3.0 Å

Source
  • uncultured cyanophage (environmental samples)
KeywordsVIRAL PROTEIN / fiber / VIRUS / baseplate / portal-adaptor / capsid asymmetric unit / Sheath-tube

+
About EMN 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

-
Oct 5, 2021. Nobel Prize for mechanically activated and temperature-gated ion channels

Nobel Prize for mechanically activated and temperature-gated ion channels

  • The Nobel Prize in Physiology or Medicine 2021 was awarded jointly to David Julius and Ardem Patapoutian "for their discoveries of receptors for temperature and touch."
  • EM Navigator can help to find cryo-EM structure data by both pioneers.

External links:The Nobel Prize in Physiology or Medicine 2021 - NobelPrize.org / Structure data by Ardem Patapoutian / Structure data by David Julius

+
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

+
Jul 5, 2019. Downlodablable text data

Downlodablable text data

Some data of EM Navigator services can be downloaded as text file. Software such as Excel can load the data files.

PageDataFormat
EMN Searchsearch resultCSV, TSV, or JSON
EMN statisticsdata tableCSV or TSV

Related info.:EMN Search / EMN Statistics

-
EMN Papers

Database of articles cited by 3DEM data entries

  • Database of articles cited by 3DEM data entries in EMDB and PDB
  • Using PubMed data

Related info.:EMDB / PDB / Q: What are the data sources of EM Navigator? / EM Navigator / Yorodumi Papers / Changes in new EM Navigator and Yorodumi

Read more