7MID

Sub-complex of Cas4-Cas1-Cas2 bound PAM containing DNA

Summary for 7MID

• Entry DOI: 10.2210/pdb7mid/pdb
• EMDB information: 23839 23840 23843 23845 23847
• Descriptor: CRISPR-associated exonuclease Cas4/endonuclease Cas1 fusion, CRISPR-associated endoribonuclease Cas2, DNA (5'-D(P*CP*AP*CP*CP*AP*TP*CP*GP*TP*GP*AP*GP*GP*CP*CP*TP*CP*AP*GP*CP*TP*AP*CP*G)-3'), ... (6 entities in total)
• Functional Keywords: crispr/cas, cas4, pam recognition, hydrolase-dna complex, hydrolase/dna
• Biological source: Geobacter sulfurreducens; More
• Total number of polymer chains: 6
• Total formula weight: 170672.08

Authors

Hu, C.Y.,Ke, A.K. (deposition date: 2021-04-16, release date: 2021-11-17)

Primary citation

Hu, C.,Almendros, C.,Nam, K.H.,Costa, A.R.,Vink, J.N.A.,Haagsma, A.C.,Bagde, S.R.,Brouns, S.J.J.,Ke, A.
Mechanism for Cas4-assisted directional spacer acquisition in CRISPR-Cas.
Nature, 598:515-520, 2021

PubMed Abstract: Prokaryotes adapt to challenges from mobile genetic elements by integrating spacers derived from foreign DNA in the CRISPR array. Spacer insertion is carried out by the Cas1-Cas2 integrase complex. A substantial fraction of CRISPR-Cas systems use a Fe-S cluster containing Cas4 nuclease to ensure that spacers are acquired from DNA flanked by a protospacer adjacent motif (PAM) and inserted into the CRISPR array unidirectionally, so that the transcribed CRISPR RNA can guide target searching in a PAM-dependent manner. Here we provide a high-resolution mechanistic explanation for the Cas4-assisted PAM selection, spacer biogenesis and directional integration by type I-G CRISPR in Geobacter sulfurreducens, in which Cas4 is naturally fused with Cas1, forming Cas4/Cas1. During biogenesis, only DNA duplexes possessing a PAM-embedded 3'-overhang trigger Cas4/Cas1-Cas2 assembly. During this process, the PAM overhang is specifically recognized and sequestered, but is not cleaved by Cas4. This 'molecular constipation' prevents the PAM-side prespacer from participating in integration. Lacking such sequestration, the non-PAM overhang is trimmed by host nucleases and integrated to the leader-side CRISPR repeat. Half-integration subsequently triggers PAM cleavage and Cas4 dissociation, allowing spacer-side integration. Overall, the intricate molecular interaction between Cas4 and Cas1-Cas2 selects PAM-containing prespacers for integration and couples the timing of PAM processing with the stepwise integration to establish directionality.

PubMed: 34588691
DOI: 10.1038/s41586-021-03951-z

Experimental method

ELECTRON MICROSCOPY (3.56 Å)