6WC0 image
Entry Detail
PDB ID:
6WC0
Keywords:
RNA BINDING PROTEIN/RNA/DNA
Title:
Crystal structure of AceCas9 bound with guide RNA and DNA with 5'-NNNTC-3' PAM
Biological Source:
Source Organism:
Acidothermus cellulolyticus (strain ATCC 43068 / 11B), synthetic construct
Host Organism:
Escherichia coli BL21
PDB Version:
Deposition Date:
2020-03-28
Release Date:
2020-11-18
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.61 Å
R-Value Free:
0.30
R-Value Work:
0.23
R-Value Observed:
0.24
Space Group:
P 21 21 21
6WC0 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Description:CRISPR-associated endonuclease, Csn1 family
Chain IDs:A
Chain Length:983
Number of Molecules:1
Biological Source:Acidothermus cellulolyticus (strain ATCC 43068 / 11B)
UniProt ID:A0LWB3 Pfam ID:PF18470, PF18541, PF17893, PF17894, PF18525
Polymer Type:polyribonucleotide
Description:sgRNA (95-MER)
Chain IDs:B
Chain Length:94
Number of Molecules:1
Biological Source:Acidothermus cellulolyticus 11B
Polymer Type:polydeoxyribonucleotide
Description:DNA (30-MER)
Chain IDs:C
Chain Length:30
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*AP*TP*AP*CP*TP*TP*GP*GP*CP*G)-3')
Chain IDs:D
Chain Length:10
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
NA
Primary Citation
The molecular basis for recognition of 5'-NNNCC-3' PAM and its methylation state by Acidothermus cellulolyticus Cas9.
Nat Commun 11 6346 6346 (2020)
PMID: 33311465 DOI: 10.1038/s41467-020-20204-1

Abstact

Acidothermus cellulolyticus CRISPR-Cas9 (AceCas9) is a thermophilic Type II-C enzyme that has potential genome editing applications in extreme environments. It cleaves DNA with a 5'-NNNCC-3' Protospacer Adjacent Motif (PAM) and is sensitive to its methylation status. To understand the molecular basis for the high specificity of AceCas9 for its PAM, we determined two crystal structures of AceCas9 lacking its HNH domain (AceCas9-ΔHNH) bound with a single guide RNA and DNA substrates, one with the correct and the other with an incorrect PAM. Three residues, Glu1044, Arg1088, Arg1091, form an intricate hydrogen bond network with the first cytosine and the two opposing guanine nucleotides to confer specificity. Methylation of the first but not the second cytosine base abolishes AceCas9 activity, consistent with the observed PAM recognition pattern. The high sensitivity of AceCas9 to the modified cytosine makes it a potential device for detecting epigenomic changes in genomes.

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Disease

Primary Citation of related structures
6WBR