[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

TitleStructural insights into context-dependent inhibitory mechanisms of chloramphenicol in cells.
Journal, issue, pagesNat Struct Mol Biol, Vol. 32, Issue 2, Page 257-267, Year 2025
Publish dateDec 12, 2024
AuthorsLiang Xue / Christian M T Spahn / Magdalena Schacherl / Julia Mahamid /
PubMed AbstractRibosome-targeting antibiotics represent an important class of antimicrobial drugs. Chloramphenicol (Cm) is a well-studied ribosomal peptidyl transferase center (PTC) binder and growing evidence ...Ribosome-targeting antibiotics represent an important class of antimicrobial drugs. Chloramphenicol (Cm) is a well-studied ribosomal peptidyl transferase center (PTC) binder and growing evidence suggests that its inhibitory action depends on the sequence of the nascent peptide. How such selective inhibition on the molecular scale manifests on the cellular level remains unclear. Here, we use cryo-electron tomography to analyze the impact of Cm inside the bacterium Mycoplasma pneumoniae. By resolving the Cm-bound ribosomes to 3.0 Å, we elucidate Cm's coordination with natural nascent peptides and transfer RNAs in the PTC. We find that Cm leads to the accumulation of a number of translation elongation states, indicating ongoing futile accommodation cycles, and to extensive ribosome collisions. We, thus, suggest that, beyond its direct inhibition of protein synthesis, the action of Cm may involve the activation of cellular stress responses. This work exemplifies how in-cell structural biology can expand the understanding of mechanisms of action for extensively studied antibiotics.
External linksNat Struct Mol Biol / PubMed:39668257 / PubMed Central
MethodsEM (subtomogram averaging)
Resolution2.9 - 15.0 Å
Structure data

17132

8p7x

EMDB-17132: 3.0Angstrom 70S ribosome map in chloramphenicol-treated Mycoplasma pneumoniae cells
PDB-8p7x: Mycoplasma pneumoniae 70S ribosome in chloramphenicol-treated cells
Method: EM (subtomogram averaging) / Resolution: 3.0 Å

17133

8p6p

EMDB-17133: 3.2Angstrom 30S ribosome focused-refined map in chloramphenicol-treated Mycoplasma pneumoniae cells
PDB-8p6p: Mycoplasma pneumoniae small ribosomal subunit in chloramphenicol-treated cells
Method: EM (subtomogram averaging) / Resolution: 3.2 Å

17134

8p8b

EMDB-17134: 2.9Angstrom 50S ribosome focused-refined map in chloramphenicol-treated Mycoplasma pneumoniae cells
PDB-8p8b: Mycoplasma pneumoniae large ribosomal subunit in chloramphenicol-treated cells
Method: EM (subtomogram averaging) / Resolution: 2.9 Å

17135

8p7y

EMDB-17135: 70S ribosome with additional S4-LSU in chloramphenicol-treated Mycoplasma pneumoniae cells
PDB-8p7y: Mycoplasma pneumoniae 70S ribosome with second S4 protein on large subunit
Method: EM (subtomogram averaging) / Resolution: 3.7 Å

EMDB-17136: 70S ribosome with A and P-site tRNAs in chloramphenicol-treated Mycoplasma pneumoniae cells, K3 data
Method: EM (subtomogram averaging) / Resolution: 3.6 Å

EMDB-17137: 70S ribosome with A, P and E-site tRNAs in chloramphenicol-treated Mycoplasma pneumoniae cells, K3 data
Method: EM (subtomogram averaging) / Resolution: 3.8 Å

EMDB-17138: 70S ribosome with a and P-site tRNAs in chloramphenicol-treated Mycoplasma pneumoniae cells, K3 data
Method: EM (subtomogram averaging) / Resolution: 4.4 Å

EMDB-17139: 70S ribosome with a, P and E-site tRNAs in chloramphenicol-treated Mycoplasma pneumoniae cells, K3 data
Method: EM (subtomogram averaging) / Resolution: 4.4 Å

EMDB-17140: 70S ribosome with EF-Tu-tRNA and P-site tRNA in chloramphenicol-treated Mycoplasma pneumoniae cells, K3 data
Method: EM (subtomogram averaging) / Resolution: 4.4 Å

EMDB-17141: 70S ribosome with EF-Tu-tRNA, P and E-site tRNAs in chloramphenicol-treated Mycoplasma pneumoniae cells, K3 data
Method: EM (subtomogram averaging) / Resolution: 4.4 Å

EMDB-17142: 70S ribosome with A* and P/E-site tRNAs in chloramphenicol-treated Mycoplasma pneumoniae cells, K3 data
Method: EM (subtomogram averaging) / Resolution: 7.6 Å

EMDB-17143: polysome/di-ribosome class I in chloramphenicol-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 10.0 Å

EMDB-17144: polysome/di-ribosome class II in chloramphenicol-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 15.0 Å

17145

8p8v

8p8w

EMDB-17145: polysome/di-ribosome class III in chloramphenicol-treated Mycoplasma pneumoniae cells
PDB-8p8v: Mycoplasma pneumoniae di-ribosome in chloramphenicol-treated cells (leading 70S)
PDB-8p8w: Mycoplasma pneumoniae di-ribosome in chloramphenicol-treated cells (following 70S)
Method: EM (subtomogram averaging) / Resolution: 8.7 Å

EMDB-17146: 70S ribosome with additional S4-LSU in native untreated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 4.4 Å

EMDB-17147: free 50S with additional S4-LSU in native untreated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 7.9 Å

Chemicals

ChemComp-SPD:
SPERMIDINE

ChemComp-PUT:
1,4-DIAMINOBUTANE

ChemComp-N2P:
PENTANE-1,5-DIAMINE

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-CLM:
CHLORAMPHENICOL / antibiotic*YM

ChemComp-K:
Unknown entry

ChemComp-SPM:
SPERMINE

ChemComp-LYS:
LYSINE

Source
  • mycoplasmoides pneumoniae m129 (bacteria)
KeywordsTRANSLATION / In situ / Ribosome / Chloramphenicol / cryo-ET

+
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