[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

TitleE-site drug specificity of the human pathogen ribosome.
Journal, issue, pagesSci Adv, Vol. 8, Issue 21, Page eabn1062, Year 2022
Publish dateMay 27, 2022
AuthorsYury Zgadzay / Olga Kolosova / Artem Stetsenko / Cheng Wu / David Bruchlen / Konstantin Usachev / Shamil Validov / Lasse Jenner / Andrey Rogachev / Gulnara Yusupova / Matthew S Sachs / Albert Guskov / Marat Yusupov /
PubMed Abstract is a widespread commensal fungus with substantial pathogenic potential and steadily increasing resistance to current antifungal drugs. It is known to be resistant to cycloheximide (CHX) that binds ... is a widespread commensal fungus with substantial pathogenic potential and steadily increasing resistance to current antifungal drugs. It is known to be resistant to cycloheximide (CHX) that binds to the E-transfer RNA binding site of the ribosome. Because of lack of structural information, it is neither possible to understand the nature of the resistance nor to develop novel inhibitors. To overcome this issue, we determined the structure of the vacant 80 ribosome at 2.3 angstroms and its complexes with bound inhibitors at resolutions better than 2.9 angstroms using cryo-electron microscopy. Our structures reveal how a change in a conserved amino acid in ribosomal protein eL42 explains CHX resistance in and forms a basis for further antifungal drug development.
External linksSci Adv / PubMed:35613268 / PubMed Central
MethodsEM (single particle)
Resolution2.32 - 2.77 Å
Structure data

13737

7pzy

EMDB-13737: Cryo-EM map of the vacant Candida albicans 80S ribosome
PDB-7pzy: Structure of the vacant Candida albicans 80S ribosome
Method: EM (single particle) / Resolution: 2.32 Å

13741

7q08

EMDB-13741, PDB-7q08:
Structure of Candida albicans 80S ribosome in complex with cycloheximide
Method: EM (single particle) / Resolution: 2.56 Å

13744

7q0f

EMDB-13744: Cryo-EM map of Candida albicans 80S ribosome in complex with phyllanthoside
PDB-7q0f: Structure of Candida albicans 80S ribosome in complex with phyllanthoside
Method: EM (single particle) / Resolution: 2.64 Å

13749

7q0p

EMDB-13749: Cryo-EM map of the Candida albicans 80S ribosome in complex with anisomycin
PDB-7q0p: Structure of the Candida albicans 80S ribosome in complex with anisomycin
Method: EM (single particle) / Resolution: 2.77 Å

13750

7q0r

EMDB-13750: Cryo-EM map of the Candida albicans 80S ribosome in complex with blasticidin s
PDB-7q0r: Structure of the Candida albicans 80S ribosome in complex with blasticidin s
Method: EM (single particle) / Resolution: 2.67 Å

Chemicals

ChemComp-SPD:
SPERMIDINE / Spermidine

ChemComp-PUT:
1,4-DIAMINOBUTANE / Putrescine

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER / Water

ChemComp-3HE:
4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione / Cycloheximide

ChemComp-3K5:
3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose

ChemComp-ANM:
ANISOMYCIN / antibiotic*YM / Anisomycin

ChemComp-BLS:
BLASTICIDIN S / antibiotic*YM / Blasticidin S

Source
  • candida albicans sc5314 (yeast)
  • candida albicans (yeast)
KeywordsRIBOSOME / Candida albicans / cryo-EM / cycloheximide / drug design / phyllanthoside / anisomycin / peptidyl transferase center / blasticidin s

+
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