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	RNA targeting and cleavage by the type III-Dv CRISPR effector complex.
Journal, issue, pages	Nat Commun, Vol. 15, Issue 1, Page 3324, Year 2024
Publish date	Apr 18, 2024
Authors	Evan A Schwartz / Jack P K Bravo / Mohd Ahsan / Luis A Macias / Caitlyn L McCafferty / Tyler L Dangerfield / Jada N Walker / Jennifer S Brodbelt / Giulia Palermo / Peter C Fineran / Robert D Fagerlund / David W Taylor /
PubMed Abstract	CRISPR-Cas are adaptive immune systems in bacteria and archaea that utilize CRISPR RNA-guided surveillance complexes to target complementary RNA or DNA for destruction. Target RNA cleavage at regular ...CRISPR-Cas are adaptive immune systems in bacteria and archaea that utilize CRISPR RNA-guided surveillance complexes to target complementary RNA or DNA for destruction. Target RNA cleavage at regular intervals is characteristic of type III effector complexes. Here, we determine the structures of the Synechocystis type III-Dv complex, an apparent evolutionary intermediate from multi-protein to single-protein type III effectors, in pre- and post-cleavage states. The structures show how multi-subunit fusion proteins in the effector are tethered together in an unusual arrangement to assemble into an active and programmable RNA endonuclease and how the effector utilizes a distinct mechanism for target RNA seeding from other type III effectors. Using structural, biochemical, and quantum/classical molecular dynamics simulation, we study the structure and dynamics of the three catalytic sites, where a 2'-OH of the ribose on the target RNA acts as a nucleophile for in line self-cleavage of the upstream scissile phosphate. Strikingly, the arrangement at the catalytic residues of most type III complexes resembles the active site of ribozymes, including the hammerhead, pistol, and Varkud satellite ribozymes. Our work provides detailed molecular insight into the mechanisms of RNA targeting and cleavage by an important intermediate in the evolution of type III effector complexes.
External links	Nat Commun / PubMed:38637512 / PubMed Central
Methods	EM (single particle)
Resolution	2.5 - 3.44 Å
Structure data	40248 8s9t EMDB-40248, PDB-8s9t: CRISPR-Cas type III-D effector complex Method: EM (single particle) / Resolution: 2.52 Å 40250 8s9v EMDB-40250, PDB-8s9v: CRISPR-Cas type III-D effector complex bound to a self-target RNA in the pre-cleavage state Method: EM (single particle) / Resolution: 3.0 Å 40251 8s9x EMDB-40251, PDB-8s9x: CRISPR-Cas type III-D effector complex bound to self-target RNA in a post-cleavage state Method: EM (single particle) / Resolution: 3.44 Å EMDB-40276: CRISPR-Cas type III-D effector complex consensus map Method: EM (single particle) / Resolution: 2.52 Å EMDB-40296: CRISPR-Cas type III-D effector complex local refinement map Method: EM (single particle) / Resolution: 2.5 Å EMDB-40297: CRISPR-Cas type III-D effector complex bound to a target RNA local refinement map Method: EM (single particle) / Resolution: 2.77 Å EMDB-40298: CRISPR-Cas type III-D effector complex bound to a target RNA consensus map Method: EM (single particle) / Resolution: 2.77 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-HOH: WATER
Source	synechocystis sp. pcc 6803 (bacteria)
Keywords	RNA BINDING PROTEIN / CRISPR / CRISPR-Cas / type III / complex / RNA / crRNA / RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA complex