Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	The twist-and-squeeze activation of CARF-fused adenosine deaminase by cyclic oligoadenylates.
Journal, issue, pages	EMBO J, Vol. 44, Issue 23, Page 6919-6943, Year 2025
Publish date	Oct 17, 2025
Authors	Charlisa Whyms / Yu Zhao / Doreen Addo-Yobo / Huan He / Arthur Carl Whittington / Despoina Trasanidou / Carl Raymund P Salazar / Raymond H J Staals / Hong Li /
PubMed Abstract	The recently identified CARF (CRISPR-associated Rossman-fold) family of proteins play a critical role in prokaryotic defense, mediating cOA (cyclic oligoadenylate)-stimulated ancillary immune ...The recently identified CARF (CRISPR-associated Rossman-fold) family of proteins play a critical role in prokaryotic defense, mediating cOA (cyclic oligoadenylate)-stimulated ancillary immune responses in the type III CRISPR-Cas systems. Whereas most previously characterized CARF proteins contain nucleic acids or protein degradation effectors, a subset of the family, including the CARF-fused adenosine deaminase (ADA) (Cad1), has recently been shown to convert ATP to ITP. The enzymatic mechanism and the activation process of Cad1, however, remain incompletely understood. Here we present biochemical and structural analyses of a ring nuclease Cad1, revealing its substrate binding specificity and a sequential activation process by cOAs. Despite an overall structural similarity to canonical ADA enzymes, the ADA domain of Cad1 possesses unique structural features that confer a specificity for ATP. Supported by mutational analysis, our structural work demonstrates an allosteric link between the cOA-binding CARF and the ADA domain through a protein network within the hexameric enzyme assembly. Binding of a cA4 molecule to paired CARF domains induces a twisting of the linked ADA domains around one another, which remodels their active sites and alters interactions with neighboring ADA domains, thereby driving a sequential conformational activation mechanism.
External links	EMBO J / PubMed:41107544 / PubMed Central
Methods	EM (single particle)
Resolution	2.31 - 3.17 Å
Structure data	EMDB-47886: CRISPR-associated deaminase Cad1 in cA4 bound form, symmetry expanded dimer, consensus map Method: EM (single particle) / Resolution: 2.36 Å EMDB-47887: CRISPR-associated deaminase Cad1 in cA4 bound form, symmetry expanded dimer, CARF domain focus refined map Method: EM (single particle) / Resolution: 2.53 Å EMDB-47888: CRISPR-associated deaminase Cad1 in cA4 bound form, symmetry expanded dimer, deaminase domain focus refined map Method: EM (single particle) / Resolution: 2.31 Å 47890 9ebt EMDB-47890, PDB-9ebt: CRISPR-associated deaminase Cad1 in cA4 bound form, symmetry expanded dimer, refined against a composite map Method: EM (single particle) / Resolution: 2.36 Å 48116 9eka EMDB-48116, PDB-9eka: CRISPR-associated deaminase Cad1 in Apo form Method: EM (single particle) / Resolution: 3.1 Å 48405 9mmw EMDB-48405, PDB-9mmw: CRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus map Method: EM (single particle) / Resolution: 2.36 Å 70417 9of1 EMDB-70417: CryoEM structure of Cad1 in App form, symmetry expanded dimer, refined against a composite map PDB-9of1: CryoEM structure of Cad1 in Apo form, symmetry expanded dimer, refined against a composite map Method: EM (single particle) / Resolution: 2.7 Å EMDB-70419: Consensus map of Cad1 in App form Method: EM (single particle) / Resolution: 2.7 Å 70422 9ofb EMDB-70422, PDB-9ofb: CryoEM structure of Cad1 bound with cA4 and ATP, symmetry expanded dimer refined against a composite map Method: EM (single particle) / Resolution: 2.68 Å EMDB-70423: Focused map on CARF domain of Cad1 in Apo form Method: EM (single particle) / Resolution: 2.87 Å EMDB-70424: Focused map for the ADA domain of Cad1 in Apo form Method: EM (single particle) / Resolution: 2.55 Å EMDB-70425: Consensus map of Cad1 bound with cA4 and ATP Method: EM (single particle) / Resolution: 2.68 Å EMDB-70426: Focused map of the CARF domain of Cad1 bound with cA4 and ATP Method: EM (single particle) / Resolution: 2.54 Å EMDB-70427: Focused map of the ADA domain of Cad1 bound with cA4 and ATP Method: EM (single particle) / Resolution: 2.45 Å 70428 9ofc EMDB-70428, PDB-9ofc: CryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimers Method: EM (single particle) / Resolution: 3.17 Å 70429 9ofd EMDB-70429, PDB-9ofd: CryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimer Method: EM (single particle) / Resolution: 2.86 Å 70430 9ofe EMDB-70430, PDB-9ofe: CryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimers Method: EM (single particle) / Resolution: 2.68 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM ChemComp-MG: Unknown entry ChemComp-HOH*: WATER
Source	thermoanaerobaculum aquaticum (bacteria)
Keywords	SIGNALING PROTEIN / CRISPR-associated CARF ring nuclease / Cad1 / CRISPR-associated adenosine deaminase / S-adenosylmethionine / HYDROLASE / ANTIVIRAL PROTEIN/RNA / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-RNA complex / IMMUNE SYSTEM / CRISPR-associated Rossman-fold (CARF) / ATP deaminase / CRISPR immunity / cooperative activation