Extended Data Fig. 10: Structural analysis of OpenCRISPR-1.
From: Design of highly functional genome editors by modelling CRISPR–Cas sequences
The structure of the OpenCRISPR1 protein was predicted with AlphaFold230 using multiple-sequence alignments from ColabFoldDB61 and template structure of SpCas9’s catalytic state (PDB: 7Z4J). The predicted protein structure was aligned to complex with the sgRNA and DNA. a) Structural model of OpenCRISPR-1 effector complex in catalytic state. Insertions in the HNH and REC1 domains with potential functional implications are highlighted. b) Analysis of OpenCRISPR-1 mutational distribution relative to SpCas9 according to residue burial (top) and whether a residue is in contact (<4.0 Å) with nucleic acids (bottom). Residue burial was not a significant determinant of mutational distribution, while nucleic-acid contacting residues were significantly depleted in mutations (chi-squared contingency test, p < 0.05). c) Nine-residue positively charged insertion in the REC1 domain of OpenCRISPR-1, which introduces stabilizing interactions with the phosphate backbone of the guide RNA’s repeat:anti-repeat segment and the target DNA’s PAM-proximal region. d) Four-residue insertion in the HNH domain of OpenCRISPR-1 modeled in the checkpoint state (PDB: 7Z4L), which may serve to stabilize the cleavage checkpoint state.
