RCSB PDB - 7UQ2: Vs.4 from T4 phage in complex with cGAMP

 7UQ2

Vs.4 from T4 phage in complex with cGAMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.206 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 

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This is version 1.4 of the entry. See complete history


Literature

Ubiquitin-like conjugation by bacterial cGAS enhances anti-phage defence.

Jenson, J.M.Li, T.Du, F.Ea, C.K.Chen, Z.J.

(2023) Nature 616: 326-331

  • DOI: https://doi.org/10.1038/s41586-023-05862-7
  • Primary Citation of Related Structures:  
    7UQ2

  • PubMed Abstract: 

    cGAS is an evolutionarily conserved enzyme that has a pivotal role in immune defence against infection 1-3 . In vertebrate animals, cGAS is activated by DNA to produce cyclic GMP-AMP (cGAMP) 4,5 , which leads to the expression of antimicrobial genes 6,7 . In bacteria, cyclic dinucleotide (CDN)-based anti-phage signalling systems (CBASS) have been discovered 8-11 . These systems are composed of cGAS-like enzymes and various effector proteins that kill bacteria on phage infection, thereby stopping phage spread. Of the CBASS systems reported, approximately 39% contain Cap2 and Cap3, which encode proteins with homology to ubiquitin conjugating (E1/E2) and deconjugating enzymes, respectively 8,12 . Although these proteins are required to prevent infection of some bacteriophages 8 , the mechanism by which the enzymatic activities exert an anti-phage effect is unknown. Here we show that Cap2 forms a thioester bond with the C-terminal glycine of cGAS and promotes conjugation of cGAS to target proteins in a process that resembles ubiquitin conjugation. The covalent conjugation of cGAS increases the production of cGAMP. Using a genetic screen, we found that the phage protein Vs.4 antagonized cGAS signalling by binding tightly to cGAMP (dissociation constant of approximately 30 nM) and sequestering it. A crystal structure of Vs.4 bound to cGAMP showed that Vs.4 formed a hexamer that was bound to three molecules of cGAMP. These results reveal a ubiquitin-like conjugation mechanism that regulates cGAS activity in bacteria and illustrates an arms race between bacteria and viruses through controlling CDN levels.


  • Organizational Affiliation

    Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vs.4
A, B, C, D, E
89TequatrovirusMutation(s): 0 
Gene Names: y06G62.5vs.4
UniProt
Find proteins for P13314 (Enterobacteria phage T4)
Explore P13314 
Go to UniProtKB:  P13314
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13314
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4BW (Subject of Investigation/LOI)
Query on 4BW

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
L [auth C]
2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one
C20 H24 N10 O13 P2
RFCBNSCSPXMEBK-INFSMZHSSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
M [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.694α = 90
b = 81.694β = 90
c = 217.616γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 4BWClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-08
    Type: Initial release
  • Version 1.1: 2023-03-15
    Changes: Database references
  • Version 1.2: 2023-04-26
    Changes: Database references
  • Version 1.3: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary