9G12 | pdb_00009g12

Mycobacterium tuberculosis RelBE1 toxin-antitoxin system; rv1247c (relB1 antitoxin), rv1246c (relE1 toxin)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.268 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.251 (DCC) 
  • R-Value Observed: 
    0.241 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9G12

This is version 1.0 of the entry. See complete history

Literature

Ribonuclease toxin RelE1 inhibits growth of Mycobacterium tuberculosis through specific cleavage of the ribosomal anti-Shine-Dalgarno region.

Han, X.Beck, I.N.Mansour, M.Arrowsmith, T.J.Barriot, R.Chansigaud, P.Pages, C.Hamze, H.Akarsu, H.Falquet, L.Redder, P.Xu, X.Blower, T.R.Genevaux, P.

(2025) Nucleic Acids Res 53

  • DOI: https://doi.org/10.1093/nar/gkaf1070
  • Primary Citation Related Structures: 
    9G12

  • PubMed Abstract: 

    Toxin-antitoxin (TA) systems are central to bacterial immunity, genome maintenance, and pathogenicity. Toxins of TA systems use diverse strategies to control bacterial growth and represent attractive therapeutic targets to fight pathogens. In this work, we have investigated the toxic mechanism of the three RelE toxins of Mycobacterium tuberculosis, the bacterium responsible for tuberculosis in humans. Structural studies showed that RelBE1, RelBE2, and RelBE3 TA complexes share conserved structural motifs distinct from the RelBE complex of Escherichia coli. Although RelE homologs have previously been reported to perform ribosome-dependent messenger RNA (mRNA) cleavage, detection of cleavage products by nEMOTE demonstrated that only RelE3 targets mRNA. In contrast, in vitro and in vivo analyses using Mycobacterium smegmatis and M. tuberculosis revealed that RelE1 is a site-specific RNase, able to cleave 16S rRNA from free 30S and formed 70S ribosomes, to release the anti-Shine-Dalgarno region and prevent translation. This stunning mode of action, which is likely shared with RelE2, demonstrates that there is broader diversity for toxic mechanisms within the widespread RelE family.


  • Organizational Affiliation
    • Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062, Toulouse, France.

Macromolecule Content 

  • Total Structure Weight: 41.77 kDa 
  • Atom Count: 2,686 
  • Modeled Residue Count: 343 
  • Deposited Residue Count: 372 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Toxin RelE
A, B
97Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: relErelE1Rv1246c
EC: 3.1
UniProt
Find proteins for O50461 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O50461 
Go to UniProtKB:  O50461
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO50461
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Antitoxin RelB
C, D
89Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: relBrelB1Rv1247c
UniProt
Find proteins for O50462 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O50462 
Go to UniProtKB:  O50462
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO50462
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
(Subject of Investigation/LOI)

Query on CL



Download:Ideal Coordinates CCD File
E [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.268 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.251 (DCC) 
  • R-Value Observed: 0.241 (Depositor) 
Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.989α = 90
b = 98.541β = 90
c = 97.345γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release