6LG3 | pdb_00006lg3

Crystal structure of a bacterial toxin from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.244 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Mycobacterial EST12 activates a RACK1-NLRP3-gasdermin D pyroptosis-IL-1 beta immune pathway.

Qu, Z.Zhou, J.Zhou, Y.Xie, Y.Jiang, Y.Wu, J.Luo, Z.Liu, G.Yin, L.Zhang, X.L.

(2020) Sci Adv 6

  • DOI: https://doi.org/10.1126/sciadv.aba4733
  • Primary Citation Related Structures: 
    6LG3

  • PubMed Abstract: 

    Pyroptosis, an inflammatory form of programmed cell death, has been implicated in eliminating pathogenic infections. However, macrophage pyroptosis-related proteins from Mycobacterium tuberculosis ( M.tb ) have largely gone unexplored. Here, we identified a cell pyroptosis-inducing protein, Rv1579c, named EST12, secreted from the M.tb H37Rv region of difference 3. EST12 binds to the receptor for activated C kinase 1 (RACK1) in macrophages, and the EST12-RACK1 complex recruits the deubiquitinase UCHL5 to promote the K48-linked deubiquitination of NLRP3, subsequently leading to an NLRP3 inflammasome caspase-1/11-pyroptosis gasdermin D-interleukin-1β immune process. Analysis of the crystal structure of EST12 reveals that the amino acid Y80 acts as a critical binding site for RACK1. An EST12-deficient strain (H37RvΔEST12) displayed higher susceptibility to M.tb infection in vitro and in vivo. These results provide the first proof that RACK1 acts as an endogenous host sensor for pathogens and that EST12-RACK1-induced pyroptosis plays a pivotal role in M.tb -induced immunity.


  • Organizational Affiliation
    • Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology of School of Basic Medical Sciences and Department of Allergy of Zhongnan Hospital, Wuhan University, Wuhan 430071, China.

Macromolecule Content 

  • Total Structure Weight: 8.04 kDa 
  • Atom Count: 608 
  • Modeled Residue Count: 74 
  • Deposited Residue Count: 74 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PhiRv1 phage protein74Mycobacterium tuberculosisMutation(s): 0 
UniProt
Find proteins for O06611 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O06611 
Go to UniProtKB:  O06611
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06611
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.244 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 26.539α = 90
b = 60.14β = 107.847
c = 28.121γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina--

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description