9NWN | pdb_00009nwn

Structure of minimal CRISPR polymerase bound to ApNHpp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 
    0.249 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: in silico
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This is version 1.1 of the entry. See complete history


Literature

A miniature CRISPR-Cas10 enzyme confers immunity by inhibitory signalling.

Doherty, E.E.Adler, B.A.Yoon, P.H.Hsieh, K.Loi, K.Armbruster, E.G.Lahiri, A.Bolling, C.S.Wilcox, X.E.Akkati, A.Iavarone, A.T.Pogliano, J.Doudna, J.A.

(2025) Nature 647: 997-1004

  • DOI: https://doi.org/10.1038/s41586-025-09569-9
  • Primary Citation Related Structures: 
    9NWN

  • PubMed Abstract: 

    Microbial and viral co-evolution has created immunity mechanisms involving oligonucleotide signalling that share mechanistic features with human antiviral systems 1 . In these pathways, including cyclic oligonucleotide-based antiphage signalling systems (CBASSs) and type III CRISPR systems in bacteria and cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) in humans, oligonucleotide synthesis occurs upon detection of virus or foreign genetic material in the cell, triggering the antiviral response 2-4 . Here, in an unexpected inversion of this process, we show that the CRISPR-related enzyme mCpol synthesizes cyclic oligonucleotides constitutively as part of an active mechanism that represses a toxic effector. Cell-based experiments demonstrated that the absence or loss of mCpol-produced cyclic oligonucleotides triggers cell death, preventing the spread of viruses that attempt immune evasion by depleting host cyclic nucleotides. Structural and mechanistic investigation revealed mCpol to be a di-adenylate cyclase whose product, c-di-AMP, prevents toxic oligomerization of the effector protein 2TMβ. Analysis of cells by fluorescence microscopy showed that lack of mCpol allows 2TMβ-mediated cell death due to inner membrane collapse. These findings unveil a powerful defence strategy against virus-mediated immune suppression, expanding our understanding of the role of oligonucleotides in immunity.


  • Organizational Affiliation
    • Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MCpol domain-containing proteinA [auth B],
B [auth A]
125Escherichia coliMutation(s): 0 
Gene Names: DU321_04150
UniProt
Find proteins for A0A426EXS8 (Escherichia coli)
Explore A0A426EXS8 
Go to UniProtKB:  A0A426EXS8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A426EXS8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.135α = 90
b = 56.769β = 90
c = 93.705γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF32GM153031

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release
  • Version 1.1: 2026-03-11
    Changes: Database references