[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

TitleExit tunnel modulation as resistance mechanism of S. aureus erythromycin resistant mutant.
Journal, issue, pagesSci Rep, Vol. 9, Issue 1, Page 11460, Year 2019
Publish dateAug 7, 2019
AuthorsYehuda Halfon / Donna Matzov / Zohar Eyal / Anat Bashan / Ella Zimmerman / Jette Kjeldgaard / Hanne Ingmer / Ada Yonath /
PubMed AbstractThe clinical use of the antibiotic erythromycin (ery) is hampered owing to the spread of resistance genes that are mostly mutating rRNA around the ery binding site at the entrance to the protein exit ...The clinical use of the antibiotic erythromycin (ery) is hampered owing to the spread of resistance genes that are mostly mutating rRNA around the ery binding site at the entrance to the protein exit tunnel. Additional effective resistance mechanisms include deletion or insertion mutations in ribosomal protein uL22, which lead to alterations of the exit tunnel shape, located 16 Å away from the drug's binding site. We determined the cryo-EM structures of the Staphylococcus aureus 70S ribosome, and its ery bound complex with a two amino acid deletion mutation in its ß hairpin loop, which grants the bacteria resistance to ery. The structures reveal that, although the binding of ery is stable, the movement of the flexible shorter uL22 loop towards the tunnel wall creates a wider path for nascent proteins, thus enabling bypass of the barrier formed by the drug. Moreover, upon drug binding, the tunnel widens further.
External linksSci Rep / PubMed:31391518 / PubMed Central
MethodsEM (single particle)
Resolution2.3 - 3.58 Å
Structure data

10076

6s0x

EMDB-10076, PDB-6s0x:
Erythromycin Resistant Staphylococcus aureus 70S ribosome (delta R88 A89 uL22) in complex with erythromycin.
Method: EM (single particle) / Resolution: 2.425 Å

10077

6s0z

EMDB-10077, PDB-6s0z:
Erythromycin Resistant Staphylococcus aureus 50S ribosome (delta R88 A89 uL22) in complex with erythromycin.
Method: EM (single particle) / Resolution: 2.3 Å

10078

6s12

EMDB-10078, PDB-6s12:
Erythromycin Resistant Staphylococcus aureus 50S ribosome (delta R88 A89 uL22).
Method: EM (single particle) / Resolution: 3.2 Å

10079

6s13

EMDB-10079, PDB-6s13:
Erythromycin Resistant Staphylococcus aureus 70S ribosome (delta R88 A89 uL22).
Method: EM (single particle) / Resolution: 3.58 Å

Chemicals

ChemComp-ERY:
ERYTHROMYCIN A / antibiotic*YM

Source
  • staphylococcus aureus (bacteria)
KeywordsRIBOSOME / antibiotics / resistance / Staphylococcus aureus / exit tunnel / RNA / rProteins / erythromycin

+
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