Computational protocol: Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not by type V CRISPR–Cas effector complexes

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Protocol publication

[…] Structural coordinates of glucosyl-5-hydroxymethyl modified thymine was isolated from an existing model (PDB 308D; ()). The modified nucleotide was statically modelled onto target strand (TS) and non-target strand (NTS) nucleotides in structures of E. coli Cascade (PDB: 5H9F; ()), S. pyogenes Cas9 (PDB: 5F9R; ()), and F. novicida Cas12a (PDB: 5NFV; ()) in WinCoot 0.8.3 using Least Squares Fit Superpose. Clashes between the DNA modifications and the polypeptide chain were identified using the MolProbity () output of the Comprehensive Validation Tool within Phenix (). Identified clashes between the glucosyl-5-hydroxymethyl modification and polypeptide residues are schematically indicated in Figure . […]

Pipeline specifications

Software tools MolProbity, PHENIX
Application Protein structure analysis
Organisms Filamentous phage, Escherichia virus T4