Structures of Neisseria meningitidis Cas9 Complexes in Catalytically Poised and Anti-CRISPR-Inhibited States

Mol Cell. 2019 Dec 19;76(6):938-952.e5. doi: 10.1016/j.molcel.2019.09.025. Epub 2019 Oct 24.


High-resolution Cas9 structures have yet to reveal catalytic conformations due to HNH nuclease domain positioning away from the cleavage site. Nme1Cas9 and Nme2Cas9 are compact nucleases for in vivo genome editing. Here, we report structures of meningococcal Cas9 homologs in complex with sgRNA, dsDNA, or the AcrIIC3 anti-CRISPR protein. DNA-bound structures represent an early step of target recognition, a later HNH pre-catalytic state, the HNH catalytic state, and a cleaved-target-DNA-bound state. In the HNH catalytic state of Nme1Cas9, the active site is seen poised at the scissile phosphodiester linkage of the target strand, providing a high-resolution view of the active conformation. The HNH active conformation activates the RuvC domain. Our structures explain how Nme1Cas9 and Nme2Cas9 read distinct PAM sequences and how AcrIIC3 inhibits Nme1Cas9 activity. These structures provide insights into Cas9 domain rearrangements, guide-target engagement, cleavage mechanism, and anti-CRISPR inhibition, facilitating the optimization of these genome-editing platforms.

Keywords: AcrIIC3; HNH domain; Nme1Cas9; Nme2Cas9; PAM; anti-CRISPR; catalytic state; genome editing; sgRNA.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Video-Audio Media

MeSH terms

  • Bacteriophages / genetics
  • Bacteriophages / metabolism*
  • Binding Sites
  • CRISPR-Associated Protein 9 / genetics
  • CRISPR-Associated Protein 9 / metabolism*
  • CRISPR-Associated Protein 9 / ultrastructure
  • CRISPR-Cas Systems*
  • Catalysis
  • Clustered Regularly Interspaced Short Palindromic Repeats*
  • DNA / genetics
  • DNA / metabolism*
  • DNA / ultrastructure
  • Escherichia coli / enzymology
  • Escherichia coli / genetics
  • Neisseria meningitidis / enzymology*
  • Neisseria meningitidis / genetics
  • Protein Binding
  • Protein Domains
  • RNA, Guide, CRISPR-Cas Systems / genetics
  • RNA, Guide, CRISPR-Cas Systems / metabolism
  • Structure-Activity Relationship
  • Viral Proteins / genetics
  • Viral Proteins / metabolism*
  • Viral Proteins / ultrastructure


  • RNA, Guide, CRISPR-Cas Systems
  • Viral Proteins
  • DNA
  • CRISPR-Associated Protein 9