8SMG

Structure of SPO1 phage Tad2 in complex with 1''-2' gcADPR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Phages overcome bacterial immunity via diverse anti-defence proteins.

Yirmiya, E.Leavitt, A.Lu, A.Ragucci, A.E.Avraham, C.Osterman, I.Garb, J.Antine, S.P.Mooney, S.E.Hobbs, S.J.Kranzusch, P.J.Amitai, G.Sorek, R.

(2024) Nature 625: 352-359

  • DOI: https://doi.org/10.1038/s41586-023-06869-w
  • Primary Citation of Related Structures:  
    8SMD, 8SME, 8SMF, 8SMG, 8TTO

  • PubMed Abstract: 

    It was recently shown that bacteria use, apart from CRISPR-Cas and restriction systems, a considerable diversity of phage resistance systems 1-4 , but it is largely unknown how phages cope with this multilayered bacterial immunity. Here we analysed groups of closely related Bacillus phages that showed differential sensitivity to bacterial defence systems, and discovered four distinct families of anti-defence proteins that inhibit the Gabija, Thoeris and Hachiman systems. We show that these proteins Gad1, Gad2, Tad2 and Had1 efficiently cancel the defensive activity when co-expressed with the respective defence system or introduced into phage genomes. Homologues of these anti-defence proteins are found in hundreds of phages that infect taxonomically diverse bacterial species. We show that the anti-Gabija protein Gad1 blocks the ability of the Gabija defence complex to cleave phage-derived DNA. Our data further reveal that the anti-Thoeris protein Tad2 is a 'sponge' that sequesters the immune signalling molecules produced by Thoeris TIR-domain proteins in response to phage infection. Our results demonstrate that phages encode an arsenal of anti-defence proteins that can disable a variety of bacterial defence mechanisms.


  • Organizational Affiliation

    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gp34.65
A, B
90OkubovirusMutation(s): 0 
Gene Names: 34.65
UniProt
Find proteins for B6V311 (Bacillus phage SP01)
Explore B6V311 
Go to UniProtKB:  B6V311
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6V311
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MF6 (Subject of Investigation/LOI)
Query on MF6

Download Ideal Coordinates CCD File 
C [auth B](1S,3R,4R,6R,9S,11R,14R,15S,16R,18R)-4-(6-amino-9H-purin-9-yl)-9,11,15,16,18-pentahydroxy-2,5,8,10,12,17-hexaoxa-9lambda~5~,11lambda~5~-diphosphatricyclo[12.2.1.1~3,6~]octadecane-9,11-dione
C15 H21 N5 O13 P2
FWMYLCHFFTZWAN-ZQSHOCFMSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.064α = 90
b = 108.064β = 90
c = 72.357γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--
Israel Science FoundationIsrael--
German Research Foundation (DFG)Germany--
The Pew Charitable TrustsUnited States--
The G. Harold and Leila Y. Mathers FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release
  • Version 1.1: 2023-12-13
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Database references