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	Cas12a domain flexibility guides R-loop formation and forces RuvC resetting.
Journal, issue, pages	Mol Cell, Vol. 84, Issue 14, Page 2717-22731.e6, Year 2024
Publish date	Jul 25, 2024
Authors	Isabel Strohkendl / Aakash Saha / Catherine Moy / Alexander-Hoi Nguyen / Mohd Ahsan / Rick Russell / Giulia Palermo / David W Taylor /
PubMed Abstract	The specific nature of CRISPR-Cas12a makes it a desirable RNA-guided endonuclease for biotechnology and therapeutic applications. To understand how R-loop formation within the compact Cas12a enables ...The specific nature of CRISPR-Cas12a makes it a desirable RNA-guided endonuclease for biotechnology and therapeutic applications. To understand how R-loop formation within the compact Cas12a enables target recognition and nuclease activation, we used cryo-electron microscopy to capture wild-type Acidaminococcus sp. Cas12a R-loop intermediates and DNA delivery into the RuvC active site. Stages of Cas12a R-loop formation-starting from a 5-bp seed-are marked by distinct REC domain arrangements. Dramatic domain flexibility limits contacts until nearly complete R-loop formation, when the non-target strand is pulled across the RuvC nuclease and coordinated domain docking promotes efficient cleavage. Next, substantial domain movements enable target strand repositioning into the RuvC active site. Between cleavage events, the RuvC lid conformationally resets to occlude the active site, requiring re-activation. These snapshots build a structural model depicting Cas12a DNA targeting that rationalizes observed specificity and highlights mechanistic comparisons to other class 2 effectors.
External links	Mol Cell / PubMed:38955179 / PubMed Central
Methods	EM (single particle)
Resolution	3.3 - 3.8 Å
Structure data	40441 8sfh EMDB-40441, PDB-8sfh: WT CRISPR-Cas12a with a 5bp R-loop Method: EM (single particle) / Resolution: 3.4 Å 40442 8sfi EMDB-40442, PDB-8sfi: WT CRISPR-Cas12a with a 8bp R-loop Method: EM (single particle) / Resolution: 3.5 Å 40443 8sfj EMDB-40443, PDB-8sfj: WT CRISPR-Cas12a with a 10bp R-loop Method: EM (single particle) / Resolution: 3.6 Å 40444 8sfl EMDB-40444, PDB-8sfl: WT CRISPR-Cas12a with a 15bp R-loop Method: EM (single particle) / Resolution: 3.3 Å 40445 8sfn EMDB-40445, PDB-8sfn: WT CRISPR-Cas12a with a 16bp R-loop and nontarget strand in the RuvC active site. Method: EM (single particle) / Resolution: 3.3 Å 40446 8sfo EMDB-40446, PDB-8sfo: WT CRISPR-Cas12a with a 20bp R-loop and nontarget strand in the RuvC active site. Method: EM (single particle) / Resolution: 3.3 Å 40447 8sfp EMDB-40447, PDB-8sfp: WT CRISPR-Cas12a with the target strand in the RuvC active site. Method: EM (single particle) / Resolution: 3.8 Å 40448 8sfq EMDB-40448, PDB-8sfq: WT CRISPR-Cas12a post nontarget strand-cleavage with the the RuvC active site exposed. Method: EM (single particle) / Resolution: 3.5 Å 40449 8sfr EMDB-40449, PDB-8sfr: WT CRISPR-Cas12a post nontarget strand cleavage. Method: EM (single particle) / Resolution: 3.5 Å
Chemicals	ChemComp-MG: Unknown entry
Source	acidaminococcus sp. bv3l6 (bacteria) synthetic construct (others)
Keywords	DNA BINDING PROTEIN/DNA/RNA / CRISPR / R-loop / endonuclease / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA-RNA complex