Protein Family Models

This entry represent a RuvC endonuclease domain (RNAseH-like) domain found in CRISPR-Cas9 from Streptococcus pyogenes and related sequences [1-5]. This domain, and the HNH (Pfam:PF13395) domain of Cas9, are used to cleave the DNA strands complementary (target) and non-complementary (non-target) to the crRNA, respectively [5]. This domain is related to Pfam:PF18541. Paper describing PDB structure 4cmp. [1]. 24505130. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, Ma E, Anders C, Hauer M, Zhou K, Lin S, Kaplan M, Iavarone AT, Charpentier E, Nogales E, Doudna JA;. Science. 2014;343:1247997. Paper describing PDB structure 4oo8. [2]. 24529477. Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA. Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O;. Cell. 2014; [Epub ahead of print]. Paper describing PDB structure 4un3. [3]. 25079318. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Anders C, Niewoehner O, Duerst A, Jinek M;. Nature. 2014;513:569-573. Paper describing PDB structure 4zt0. [4]. 26113724. STRUCTURAL BIOLOGY. A Cas9-guide RNA complex preorganized for target DNA recognition. Jiang F, Zhou K, Ma L, Gressel S, Doudna JA;. Science. 2015;348:1477-1481. Paper describing PDB structure 5b2r. [5]. 26990991. Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9. Hirano S, Nishimasu H, Ishitani R, Nureki O;. Mol Cell. 2016;61:886-894. (from Pfam)

Date:

2024-10-16

The REC lobe of Cas9 - the CRISPR-associated endonuclease Cas9 - includes the REC1 and REC2 domains. REC1 forms an elongated, alpha-helical structure consisting of 25 alpha helices and two beta-sheets, whereas REC2 inserted within REC1 adopts a six-helix bundle structure. The REC lobe and the NUC lobe of Cas9 fold to present a positively charged groove at their interface which accommodates the negatively charged sgRNA:target DNA heteroduplex [1]. CRISPR (clustered regularly interspaced short palindromic repeat)-Cas system occurs naturally in bacteria as a defence against invasion by phages or other mobile genetic elements. Cas9 is targeted to specific genomic locations by sgRNAs or single guide RNAs, in order to complex with invading DNA in order to cleave it and render it inactive. [1]. 24529477. Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA. Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O;. Cell. 2014; [Epub ahead of print] (from Pfam)

Date:

2024-10-16

Cas9_PI is a family found at the C-terminal of bacterial type II CRISPR system Cas9 endonuclease. This domain adopts a novel protein fold that is unique to the Cas9 family. It is positioned in the structure-DNA-complex to recognise the PAM sequence on the non-complementary DNA strand of the crRNA. PAM sequence is protospacer-adjacent motifs on DNA. See family CRISPR-DR2, Rfam:RF01315. Cas9 carries two nuclease domains, HNH and RuvC, which cleave the DNA strands that are complementary and non-complementary to the 20 nucleotide guide sequence in crRNAs, respectively [1]. [1]. 24634220. Cut site selection by the two nuclease domains of the Cas9 RNA-guided endonuclease. Chen H, Choi J, Bailey S;. J Biol Chem. 2014;289:13284-13294. (from Pfam)

Date:

2024-10-16

Cas9-BH is the bridge helix between the NUC and the REC lobes of Cas9 - the CRISPR-associated endonuclease Cas9. The REC lobe and the NUC lobe of Cas9 fold to present a positively charged groove at their interface which accommodates the negatively charged sgRNA:target DNA heteroduplex [1]. CRISPR (clustered regularly interspaced short palindromic repeat)-Cas system occurs naturally in bacteria as a defence against invasion by phages or other mobile genetic elements. Cas9 is targeted to specific genomic locations by sgRNAs or single guide RNAs, in order to complex with invading DNA in order to cleave it and render it inactive. [1]. 24529477. Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA. Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O;. Cell. 2014; [Epub ahead of print] (from Pfam)

Date:

2024-10-16

This HNH nuclease domain is found in CRISPR-related proteins. (from Pfam)

Date:

2024-08-14

Cas9, originally named Csn1, is the large, multifunctional signature protein of type II CRISPR/Cas systems. It is well known even to general audiences because its RNA-guided endonuclease activity has made it a popular tool for custom editing of eukaryotic genomes.

Gene:

cas9

Date:

2024-05-30