ISDA

Deposition Date 2017-04-19

Release Date 2017-06-14

Last Version Date 2023-11-22

Entry Detail

PDB ID:

5XH6

Keywords:

HYDROLASE/RNA/DNA

Title:

Crystal structure of the Acidaminococcus sp. BV3L6 Cpf1 RVR variant in complex with crRNA and target DNA (TATA PAM)

Biological Source:

Source Organism:

Acidaminococcus sp. (strain BV3L6) (Taxon ID: 1111120)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.00 Å

R-Value Free:

0.20

R-Value Work:

0.17

R-Value Observed:

0.17

Space Group:

P 21 21 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:CRISPR-associated endonuclease Cpf1
Gene (Uniprot):cas12a
Mutations:S542R, K548V, N552R
Chain IDs:A
Chain Length:1310
Number of Molecules:1
Biological Source:Acidaminococcus sp. (strain BV3L6)

UniProt ID:U2UMQ6 Pfam ID:PF18501, PF21918, PF18516, PF18510

Polymer Type:polyribonucleotide
Molecule:crRNA
Chain IDs:B
Chain Length:43
Number of Molecules:1
Biological Source:Acidaminococcus sp. BV3L6

Polymer Type:polydeoxyribonucleotide
Molecule:Target DNA strand
Chain IDs:C
Chain Length:34
Number of Molecules:1
Biological Source:Acidaminococcus sp. BV3L6

Polymer Type:polydeoxyribonucleotide
Molecule:Non-target DNA strand
Chain IDs:D
Chain Length:10
Number of Molecules:1
Biological Source:Acidaminococcus sp. BV3L6

Ligand Molecules

EDO

Primary Citation

Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1

Nishimasu, H, Yamano, T, Gao, L, Zhang, F, Ishitani, R, Nureki, O.Show

Mol. Cell 67 139 147.e2 (2017)

PMID: 28595896 DOI: 10.1016/j.molcel.2017.04.019

Abstact

The RNA-guided Cpf1 nuclease cleaves double-stranded DNA targets complementary to the CRISPR RNA (crRNA), and it has been harnessed for genome editing technologies. Recently, Acidaminococcus sp. BV3L6 (AsCpf1) was engineered to recognize altered DNA sequences as the protospacer adjacent motif (PAM), thereby expanding the target range of Cpf1-mediated genome editing. Whereas wild-type AsCpf1 recognizes the TTTV PAM, the RVR (S542R/K548V/N552R) and RR (S542R/K607R) variants can efficiently recognize the TATV and TYCV PAMs, respectively. However, their PAM recognition mechanisms remained unknown. Here we present the 2.0 Å resolution crystal structures of the RVR and RR variants bound to a crRNA and its target DNA. The structures revealed that the RVR and RR variants primarily recognize the PAM-complementary nucleotides via the substituted residues. Our high-resolution structures delineated the altered PAM recognition mechanisms of the AsCpf1 variants, providing a basis for the further engineering of CRISPR-Cpf1.

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Primary Citation of related structures