Crystal structure of the CRISPR-Cas RNA silencing Cmr complex bound to a target analog

Takuo Osawa; Hideko Inanaga; Chikara Sato; Tomoyuki Numata

doi:10.1016/j.molcel.2015.03.018

Crystal structure of the CRISPR-Cas RNA silencing Cmr complex bound to a target analog

Mol Cell. 2015 May 7;58(3):418-30. doi: 10.1016/j.molcel.2015.03.018. Epub 2015 Apr 23.

Authors

Takuo Osawa¹, Hideko Inanaga¹, Chikara Sato¹, Tomoyuki Numata²

Affiliations

¹ Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan.
² Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan. Electronic address: t-numata@aist.go.jp.

PMID: 25921071
DOI: 10.1016/j.molcel.2015.03.018

Abstract

In prokaryotes, Clustered regularly interspaced short palindromic repeat (CRISPR)-derived RNAs (crRNAs), together with CRISPR-associated (Cas) proteins, capture and degrade invading genetic materials. In the type III-B CRISPR-Cas system, six Cas proteins (Cmr1-Cmr6) and a crRNA form an RNA silencing Cmr complex. Here we report the 2.1 Å crystal structure of the Cmr1-deficient, functional Cmr complex bound to single-stranded DNA, a substrate analog complementary to the crRNA guide. Cmr3 recognizes the crRNA 5' tag and defines the start position of the guide-target duplex, using its idiosyncratic loops. The β-hairpins of three Cmr4 subunits intercalate within the duplex, causing nucleotide displacements with 6 nt intervals, and thus periodically placing the scissile bonds near the crucial aspartate of Cmr4. The structure reveals the mechanism for specifying the periodic target cleavage sites from the crRNA 5' tag and provides insights into the assembly of the type III interference machineries and the evolution of the Cmr and Cascade complexes.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Sequence
Archaeal Proteins / chemistry*
Archaeal Proteins / genetics
Archaeal Proteins / metabolism
Archaeoglobus fulgidus / genetics
Archaeoglobus fulgidus / metabolism
CRISPR-Associated Proteins / chemistry*
CRISPR-Associated Proteins / genetics
CRISPR-Associated Proteins / metabolism
CRISPR-Cas Systems / genetics
Clustered Regularly Interspaced Short Palindromic Repeats / genetics
Crystallography, X-Ray
Models, Molecular
Molecular Sequence Data
Nucleic Acid Conformation
Protein Binding
Protein Isoforms / chemistry
Protein Isoforms / genetics
Protein Isoforms / metabolism
Protein Structure, Tertiary
Pyrococcus furiosus / genetics
Pyrococcus furiosus / metabolism
RNA Interference*
RNA, Archaeal / chemistry*
RNA, Archaeal / genetics
RNA, Archaeal / metabolism
Sequence Homology, Amino Acid

Substances

Archaeal Proteins
CRISPR-Associated Proteins
Protein Isoforms
RNA, Archaeal

Associated data

PDB/3X1L