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	Structural insights into Cas9-mediated prespacer selection in CRISPR-Cas adaptation.
Journal, issue, pages	Mol Cell, Vol. 86, Issue 5, Page 791-804.e9, Year 2026
Publish date	Mar 5, 2026
Authors	Ugne Gaizauskaite / Giedre Tamulaitiene / Arunas Silanskas / Giedrius Gasiunas / Virginijus Siksnys / Giedrius Sasnauskas
PubMed Abstract	During CRISPR-Cas adaptation, prokaryotic cells become immunized by the insertion of foreign DNA fragments, termed spacers, into the host genome to serve as templates for RNA-guided immunity. Spacer ...During CRISPR-Cas adaptation, prokaryotic cells become immunized by the insertion of foreign DNA fragments, termed spacers, into the host genome to serve as templates for RNA-guided immunity. Spacer acquisition relies on the Cas1-Cas2 integrase and accessory proteins, which select DNA sequences flanked by the protospacer adjacent motif (PAM) and insert them into the CRISPR array. It has been shown that in type II-A systems, selection of PAM-proximal prespacers is mediated by the effector nuclease Cas9, which forms a "supercomplex" with the Cas1-Cas2 integrase and the Csn2 protein. Here, we present cryo-electron microscopy structures of the Streptococcus thermophilus type II-A prespacer selection supercomplex in the DNA-scanning and two distinct PAM-bound configurations, providing insights into the mechanism of Cas9-mediated prespacer selection in type II-A CRISPR-Cas systems. Repurposing Cas9 by the CRISPR adaptation machinery for prespacer selection, as characterized here, demonstrates Cas9 plasticity and expands our knowledge of Cas9 biology.
External links	Mol Cell / PubMed:41702403
Methods	EM (single particle)
Resolution	2.89 - 4.25 Å
Structure data	17702 8pj9 EMDB-17702, PDB-8pj9: Cas9 bound to cognate DNA, Streptococcus thermophilus DGCC 7710 CRISPR3 system Method: EM (single particle) / Resolution: 3.24 Å 51766 9h1h EMDB-51766, PDB-9h1h: Cas1-Cas2 CRISPR integrase bound to prespacer DNA, Streptococcus thermophilus DGCC 7710 CRISPR3 system Method: EM (single particle) / Resolution: 3.06 Å 51773 9h1v EMDB-51773, PDB-9h1v: Cas1-Cas2 CRISPR integrase bound to prespacer and target DNA, Streptococcus thermophilus DGCC 7710 CRISPR3 system Method: EM (single particle) / Resolution: 2.89 Å 51787 9h21 EMDB-51787, PDB-9h21: Cas9 in complex with tracrRNA and crRNA, Streptococcus thermophilus DGCC 7710 CRISPR3 system Method: EM (single particle) / Resolution: 3.33 Å 51801 9h2g EMDB-51801, PDB-9h2g: Cas9:crRNA:tracrRNA in complex with PAM-containing non-cognate DNA, PAM-bound conformation, Streptococcus thermophilus DGCC 7710 CRISPR3 system Method: EM (single particle) / Resolution: 3.28 Å 51812 9h2m EMDB-51812, PDB-9h2m: Cas9:crRNA:tracrRNA in complex with PAM-containing non-cognate DNA, PAM-unbound conformation, Streptococcus thermophilus DGCC 7710 CRISPR3 system Method: EM (single particle) / Resolution: 3.06 Å 51900 9h6t EMDB-51900, PDB-9h6t: Partial Cas1-Cas2 CRISPR integrase complex bound to a half-integration product, Streptococcus thermophilus DGCC 7710 CRISPR3 system Method: EM (single particle) / Resolution: 2.93 Å 51909 9h72 EMDB-51909, PDB-9h72: Csn2 (point mutations Y212R, I213R and M215R) in complex with Cas1-Cas2 integrase and dsDNA, Streptococcus thermophilus DGCC 7710 CRISPR3 system Method: EM (single particle) / Resolution: 3.38 Å EMDB-52317: PAM-bound Cas9-Cas1-Cas2-Csn2 supercomplex in the docked conformation, Streptococcus thermophilus DGCC 7710 CRISPR3 system Method: EM (single particle) / Resolution: 3.73 Å EMDB-52318: PAM-bound Cas9-Cas1-Cas2-Csn2 supercomplex in the docked conformation, Streptococcus thermophilus DGCC 7710 CRISPR3 system Method: EM (single particle) / Resolution: 3.7 Å EMDB-52319: PAM-bound Cas9-Cas1-Cas2-Csn2 supercomplex in the docked conformation, Streptococcus thermophilus DGCC 7710 CRISPR3 system Method: EM (single particle) / Resolution: 4.25 Å 52320 9hp8 EMDB-52320, PDB-9hp8: PAM-bound Cas9-Cas1-Cas2-Csn2 supercomplex in the docked conformation, Streptococcus thermophilus DGCC 7710 CRISPR3 system Method: EM (single particle) / Resolution: 3.7 Å EMDB-52321: Cas9-Cas1-Cas2-Csn2 supercomplex with dsDNA in PAM-unbound conformation, Streptococcus thermophilus DGCC 7710 CRISPR3 system Method: EM (single particle) / Resolution: 3.39 Å EMDB-52322: Cas9-Cas1-Cas2-Csn2 supercomplex with dsDNA in PAM-unbound conformation, Streptococcus thermophilus DGCC 7710 CRISPR3 system Method: EM (single particle) / Resolution: 3.39 Å EMDB-52323: Cas9-Cas1-Cas2-Csn2 supercomplex with dsDNA in PAM-unbound conformation, Streptococcus thermophilus DGCC 7710 CRISPR3 system Method: EM (single particle) / Resolution: 3.85 Å 52324 9hp9 EMDB-52324, PDB-9hp9: Cas9-Cas1-Cas2-Csn2 supercomplex with dsDNA in PAM-unbound conformation, Streptococcus thermophilus DGCC 7710 CRISPR3 system Method: EM (single particle) / Resolution: 3.39 Å EMDB-52883: PAM-bound Cas9-Cas1-Cas2-Csn2 supercomplex in the locked conformation, Streptococcus thermophilus DGCC 7710 (consensus map) Method: EM (single particle) / Resolution: 3.62 Å EMDB-52884: PAM-bound Cas9-Cas1-Cas2-Csn2 supercomplex in the locked conformation, Streptococcus thermophilus DGCC 7710 CRISPR3 system Method: EM (single particle) / Resolution: 3.62 Å EMDB-52885: PAM-bound Cas9-Cas1-Cas2-Csn2 supercomplex in the locked conformation, Streptococcus thermophilus DGCC 7710 CRISPR3 system Method: EM (single particle) / Resolution: 4.2 Å 52886 9q85 EMDB-52886, PDB-9q85: PAM-bound Cas9-Cas1-Cas2-Csn2 supercomplex in the locked conformation, Streptococcus thermophilus DGCC 7710 CRISPR3 system Method: EM (single particle) / Resolution: 3.62 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-CA: Unknown entry
Source	streptococcus thermophilus dgcc 7710 (bacteria) synthetic construct (others)
Keywords	RNA BINDING PROTEIN / Cas9 / CRISPR-Cas / PAM / spacer acquisition / DNA BINDING PROTEIN / Cas1-Cas2 integrase / prespacer / CRISPR leader / CRISPR repeat / CIRSPR-Cas / Cas1 / Cas2 / CRISPR integrase / Csn2