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Recently, two anti-CRISPR proteins AcrIIA2 and AcrIIA4 have been identified, both of which potently inhibit Cas9 (SpyCas9) and LmoCas9 activity in bacteria and human cells. However, the mechanism of Cas9 inhibition remains unknown. Here the scientists report a crystal structure of SpyCas9 in complex with a single guide RNA (sgRNA) and AcrIIA4. Their results reveal the mechanism of SpyCas9 inhibition by AcrIIA4, laying a structural basis for developing "off-switch" tools of SpyCas9 to avoid unwanted genome edits within cells and tissues.