[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 host cell recognition and penetration machinery of a Staphylococcus aureus bacteriophage.
Journal, issue, pagesPLoS Pathog, Vol. 16, Issue 2, Page e1008314, Year 2020
Publish dateFeb 18, 2020
AuthorsJames L Kizziah / Keith A Manning / Altaira D Dearborn / Terje Dokland /
PubMed AbstractStaphylococcus aureus is a common cause of infections in humans. The emergence of virulent, antibiotic-resistant strains of S. aureus is a significant public health concern. Most virulence and ...Staphylococcus aureus is a common cause of infections in humans. The emergence of virulent, antibiotic-resistant strains of S. aureus is a significant public health concern. Most virulence and resistance factors in S. aureus are encoded by mobile genetic elements, and transduction by bacteriophages represents the main mechanism for horizontal gene transfer. The baseplate is a specialized structure at the tip of bacteriophage tails that plays key roles in host recognition, cell wall penetration, and DNA ejection. We have used high-resolution cryo-electron microscopy to determine the structure of the S. aureus bacteriophage 80α baseplate at 3.75 Å resolution, allowing atomic models to be built for most of the major tail and baseplate proteins, including two tail fibers, the receptor binding protein, and part of the tape measure protein. Our structure provides a structural basis for understanding host recognition, cell wall penetration and DNA ejection in viruses infecting Gram-positive bacteria. Comparison to other phages demonstrates the modular design of baseplate proteins, and the adaptations to the host that take place during the evolution of staphylococci and other pathogens.
External linksPLoS Pathog / PubMed:32069326 / PubMed Central
MethodsEM (single particle)
Resolution3.45 - 4.14 Å
Structure data

20872

6v8i

EMDB-20872: C3 symmetrical reconstruction of the Staphylococcus aureus phage 80alpha baseplate
PDB-6v8i: Composite atomic model of the Staphylococcus aureus phage 80alpha baseplate
Method: EM (single particle) / Resolution: 3.96 Å

20873

6v8i

EMDB-20873: C6 symmetrical reconstruction of the Staphylococcus aureus phage 80alpha baseplate
PDB-6v8i: Composite atomic model of the Staphylococcus aureus phage 80alpha baseplate
Method: EM (single particle) / Resolution: 3.45 Å

20874

6v8i

EMDB-20874: Lower fiber-focused reconstruction of the Staphylococcus aureus phage 80alpha baseplate
PDB-6v8i: Composite atomic model of the Staphylococcus aureus phage 80alpha baseplate
Method: EM (single particle) / Resolution: 3.69 Å

20875

6v8i

EMDB-20875: Upper fiber-focused reconstruction of the Staphylococcus aureus phage 80alpha baseplate
PDB-6v8i: Composite atomic model of the Staphylococcus aureus phage 80alpha baseplate
Method: EM (single particle) / Resolution: 4.14 Å

20876

6v8i

EMDB-20876: Receptor binding protein-focused reconstruction of the Staphylococcus aureus phage 80alpha baseplate
PDB-6v8i: Composite atomic model of the Staphylococcus aureus phage 80alpha baseplate
Method: EM (single particle) / Resolution: 3.6 Å

Chemicals

ChemComp-FE:
Unknown entry

Source
  • staphylococcus virus 80alpha
KeywordsVIRAL PROTEIN / phage tail / tail tip / tape measure protein

+
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://pdbjlvh1.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