Structure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4)

Experimental Data Snapshot

  • Resolution: 1.84 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report

This is version 2.1 of the entry. See complete history


Tetramerisation of the CRISPR ring nuclease Crn3/Csx3 facilitates cyclic oligoadenylate cleavage.

Athukoralage, J.S.McQuarrie, S.Gruschow, S.Graham, S.Gloster, T.M.White, M.F.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.57627
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Type III CRISPR systems detect foreign RNA and activate the cyclase domain of the Cas10 subunit, generating cyclic oligoadenylate (cOA) molecules that act as a second messenger to signal infection, activating nucleases that degrade the nucleic acid of both invader and host. This can lead to dormancy or cell death; to avoid this, cells need a way to remove cOA from the cell once a viral infection has been defeated. Enzymes specialised for this task are known as ring nucleases, but are limited in their distribution. Here, we demonstrate that the widespread CRISPR associated protein Csx3, previously described as an RNA deadenylase, is a ring nuclease that rapidly degrades cyclic tetra-adenylate (cA 4 ). The enzyme has an unusual cooperative reaction mechanism involving an active site that spans the interface between two dimers, sandwiching the cA 4 substrate. We propose the name Crn3 (CRISPR associated ring nuclease 3) for the Csx3 family.

  • Organizational Affiliation

    Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, United Kingdom.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein AF_1864
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
111Archaeoglobus fulgidusMutation(s): 1 
Gene Names: AF_1864
Find proteins for O28415 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O28415 
Go to UniProtKB:  O28415
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO28415
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
Cyclic tetraadenosine monophosphate (cA4)K,
L [auth M],
M [auth O],
N [auth P],
O [auth Q]
4synthetic construct
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.84 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 193.969α = 90
b = 60.364β = 116.47
c = 107.085γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom204821/Z/16/Z
Other governmentUnited KingdomBBSRC BB/S000313/1
Other governmentUnited KingdomBBSRC BB/T004789/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 2.0: 2023-12-13
    Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Refinement description