[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

TitleThe Complete Structure of the Mycobacterium smegmatis 70S Ribosome.
Journal, issue, pagesCell Rep, Vol. 20, Issue 1, Page 149-160, Year 2017
Publish dateJul 5, 2017
AuthorsJendrik Hentschel / Chloe Burnside / Ingrid Mignot / Marc Leibundgut / Daniel Boehringer / Nenad Ban /
PubMed AbstractThe ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death ...The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance. Here, we present the 3.3-Å cryo-EM structure of the 70S ribosome of Mycobacterium smegmatis, a close relative to the human pathogen Mycobacterium tuberculosis. The structure reveals two additional ribosomal proteins and localizes them to the vicinity of drug-target sites in both the catalytic center and the decoding site of the ribosome. Furthermore, we visualized actinobacterium-specific rRNA and protein expansions that extensively remodel the ribosomal surface with implications for polysome organization. Our results provide a foundation for understanding the idiosyncrasies of mycobacterial translation and reveal atomic details of the structure that will facilitate the design of anti-tubercular therapeutics.
External linksCell Rep / PubMed:28683309
MethodsEM (single particle)
Resolution3.18 - 3.45 Å
Structure data

EMDB-3748: Cryo-EM reconstruction of the small subunit of the Mycobacterium smegmatis ribosome
PDB-5o5j: Structure of the 30S small ribosomal subunit from Mycobacterium smegmatis
Method: EM (single particle) / Resolution: 3.45 Å

EMDB-3750: Cryo-EM reconstruction of the large subunit of the Mycobacterium smegmatis ribosome
PDB-5o60: Structure of the 50S large ribosomal subunit from Mycobacterium smegmatis
Method: EM (single particle) / Resolution: 3.18 Å

EMDB-3751: Cryo-EM reconstruction of the Mycobacterium smegmatis 70S ribosome
PDB-5o61: The complete structure of the Mycobacterium smegmatis 70S ribosome
Method: EM (single particle) / Resolution: 3.31 Å

Chemicals

ChemComp-MG:
MAGNESIUM ION / Magnesium

ChemComp-ZN:
ZINC ION / Zinc

ChemComp-PHE:
PHENYLALANINE / Phenylalanine

Source
  • mycobacterium smegmatis str. mc2 155 (bacteria)
KeywordsBacterial Proteins / Cryoelectron Microscopy / Mycobacterium smegmatis / Protein Domains / RNA, Ribosomal / Ribosomal Proteins / Ribosome Subunits, Large, Bacterial / RIBOSOME / translation

+
About Yorodumi Papers

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
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