9B7D | pdb_00009b7d

Structure of ThsB-Tad3 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.221 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structure-guided discovery of viral proteins that inhibit host immunity.

Yirmiya, E.Hobbs, S.J.Leavitt, A.Osterman, I.Avraham, C.Hochhauser, D.Madhala, B.Skovorodka, M.Tan, J.M.J.Toyoda, H.C.Chebotar, I.Itkin, M.Malitsky, S.Amitai, G.Kranzusch, P.J.Sorek, R.

(2025) Cell 188: 1681

  • DOI: https://doi.org/10.1016/j.cell.2024.12.035
  • Primary Citation Related Structures: 
    9B7D

  • PubMed Abstract: 

    Viruses encode proteins that inhibit host defenses, but sifting through the millions of available viral sequences for immune-modulatory proteins has been so far impractical. Here, we develop a process to systematically screen virus-encoded proteins for inhibitors that physically bind host immune proteins. Focusing on Thoeris and CBASS, bacterial defense systems that are the ancestors of eukaryotic Toll/interleukin-1 receptor (TIR) and cyclic GMP-AMP synthase (cGAS) immunity, we discover seven families of Thoeris and CBASS inhibitors, encompassing thousands of genes widespread in phages. Verified inhibitors exhibit extensive physical interactions with the respective immune protein counterpart, with all inhibitors blocking the active site of the immune protein. Remarkably, a phage-encoded inhibitor of bacterial TIR proteins can bind and inhibit distantly related human and plant immune TIRs, and a phage-derived inhibitor of bacterial cGAS-like enzymes can inhibit the human cGAS. Our results demonstrate that phages are a reservoir for immune-modulatory proteins capable of inhibiting bacterial, animal, and plant immunity.


  • Organizational Affiliation
    • Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.

Macromolecule Content 

  • Total Structure Weight: 89.99 kDa 
  • Atom Count: 6,999 
  • Modeled Residue Count: 754 
  • Deposited Residue Count: 774 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative cyclic ADP-D-ribose synthase ThsB1
A, C
193Bacillus cereusMutation(s): 0 
Gene Names: thsB1thsBII9_05449
EC: 3.2.2
UniProt
Find proteins for J8G8J6 (Bacillus cereus (strain MSX-D12))
Explore J8G8J6 
Go to UniProtKB:  J8G8J6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ8G8J6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tad3
B, D
194metagenomeMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.221 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.937α = 90
b = 80.65β = 99.84
c = 72.323γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1DP2GM146250

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-02-05
    Changes: Database references
  • Version 1.2: 2025-04-02
    Changes: Database references