[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 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics.
Journal, issue, pagesStructure, Vol. 28, Issue 10, Page 1087-11100.e3, Year 2020
Publish dateOct 6, 2020
AuthorsDavid Nicholson / Thomas A Edwards / Alex J O'Neill / Neil A Ranson /
PubMed AbstractAcinetobacter baumannii is a Gram-negative bacterium primarily associated with hospital-acquired, often multidrug-resistant (MDR) infections. The ribosome-targeting antibiotics amikacin and ...Acinetobacter baumannii is a Gram-negative bacterium primarily associated with hospital-acquired, often multidrug-resistant (MDR) infections. The ribosome-targeting antibiotics amikacin and tigecycline are among the limited arsenal of drugs available for treatment of such infections. We present high-resolution structures of the 70S ribosome from A. baumannii in complex with these antibiotics, as determined by cryoelectron microscopy. Comparison with the ribosomes of other bacteria reveals several unique structural features at functionally important sites, including around the exit of the polypeptide tunnel and the periphery of the subunit interface. The structures also reveal the mode and site of interaction of these drugs with the ribosome. This work paves the way for the design of new inhibitors of translation to address infections caused by MDR A. baumannii.
External linksStructure / PubMed:32857965 / PubMed Central
MethodsEM (single particle)
Resolution2.5 - 3.0 Å
Structure data

EMDB-10809, PDB-6yhs:
Acinetobacter baumannii ribosome-amikacin complex - 50S subunit
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-10869, PDB-6ypu:
Acinetobacter baumannii ribosome-amikacin complex - 30S subunit body
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-10892, PDB-6ys5:
Acinetobacter baumannii ribosome-amikacin complex - 30S subunit head
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-10898, PDB-6ysi:
Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-10914, PDB-6yt9:
Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit body
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-10915, PDB-6ytf:
Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head
Method: EM (single particle) / Resolution: 3.0 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-AKN:
(2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S / medication, antibiotic*YM

ChemComp-T1C:
TIGECYCLINE / medication, antibiotic*YM

Source
  • acinetobacter baumannii atcc 19606 = cip 70.34 = jcm 6841 (bacteria)
  • acinetobacter baumannii (strain atcc 19606 / dsm 30007 / cip 70.34 / jcm 6841 / nbrc 109757 / ncimb 12457 / nctc 12156 / 81) (bacteria)
  • acinetobacter baumannii (bacteria)
KeywordsRIBOSOME / antibiotic / amikacin / translation / tigecycline

+
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