7QR5 image
Entry Detail
PDB ID:
7QR5
Keywords:
Title:
SpCas9 bound to FANCF off-target6 DNA substrate
Biological Source:
PDB Version:
Deposition Date:
2022-01-17
Release Date:
2022-10-26
Method Details:
Experimental Method:
Resolution:
3.30 Å
R-Value Free:
0.25
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:FANCF sgRNA
Chain IDs:A
Chain Length:84
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polypeptide(L)
Description:CRISPR-associated endonuclease Cas9/Csn1
Mutations:D10A, H840A
Chain IDs:B
Chain Length:1368
Number of Molecules:1
Biological Source:Streptococcus pyogenes
Polymer Type:polydeoxyribonucleotide
Description:FANCF off-target6 target strand
Chain IDs:C
Chain Length:28
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:FANCF off-target6 non-target strand
Chain IDs:D
Chain Length:12
Number of Molecules:1
Biological Source:synthetic construct
Primary Citation
Structural basis for Cas9 off-target activity.
Cell 185 4067 4081.e21 (2022)
PMID: 36306733 DOI: 10.1016/j.cell.2022.09.026

Abstact

The target DNA specificity of the CRISPR-associated genome editor nuclease Cas9 is determined by complementarity to a 20-nucleotide segment in its guide RNA. However, Cas9 can bind and cleave partially complementary off-target sequences, which raises safety concerns for its use in clinical applications. Here, we report crystallographic structures of Cas9 bound to bona fide off-target substrates, revealing that off-target binding is enabled by a range of noncanonical base-pairing interactions within the guide:off-target heteroduplex. Off-target substrates containing single-nucleotide deletions relative to the guide RNA are accommodated by base skipping or multiple noncanonical base pairs rather than RNA bulge formation. Finally, PAM-distal mismatches result in duplex unpairing and induce a conformational change in the Cas9 REC lobe that perturbs its conformational activation. Together, these insights provide a structural rationale for the off-target activity of Cas9 and contribute to the improved rational design of guide RNAs and off-target prediction algorithms.

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