SNAP output for PDB entry 6vpc [SNAP web server]

PDB-id

6vpc; SNAP-derived features in text and JSON formats; DNAproDB

Class

DNA binding protein-DNA-RNA

Method

cryo-EM (3.2 Å)

Summary

Structure of the spcas9 DNA adenine base editor - abe8e

Reference

Lapinaite A, Knott GJ, Palumbo CM, Lin-Shiao E, Richter MF, Zhao KT, Beal PA, Liu DR, Doudna JA (2020): "DNA capture by a CRISPR-Cas9-guided adenine base editor." Science, 369, 566-571. doi: 10.1126/science.abb1390.

Abstract

CRISPR-Cas-guided base editors convert A•T to G•C, or C•G to T•A, in cellular DNA for precision genome editing. To understand the molecular basis for DNA adenosine deamination by adenine base editors (ABEs), we determined a 3.2-angstrom resolution cryo-electron microscopy structure of ABE8e in a substrate-bound state in which the deaminase domain engages DNA exposed within the CRISPR-Cas9 R-loop complex. Kinetic and structural data suggest that ABE8e catalyzes DNA deamination up to ~1100-fold faster than earlier ABEs because of mutations that stabilize DNA substrates in a constrained, transfer RNA-like conformation. Furthermore, ABE8e's accelerated DNA deamination suggests a previously unobserved transient DNA melting that may occur during double-stranded DNA surveillance by CRISPR-Cas9. These results explain ABE8e-mediated base-editing outcomes and inform the future design of base editors.