5XH7

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

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

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

(2017) Mol. Cell 67: 139-147.e2

  • DOI: 10.1016/j.molcel.2017.04.019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • 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 ...

    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.

    Organizational Affiliation: 

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; JST, PRESTO, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address: nisimasu@bs.s.u-tokyo.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR-associated endonuclease Cpf1
A
1310Acidaminococcus sp. (strain BV3L6)Mutation(s): 2 
Gene Names: cas12a (cpf1)
EC: 3.1.21.1, 3.1.27.2
Find proteins for U2UMQ6 (Acidaminococcus sp. (strain BV3L6))
Go to UniProtKB:  U2UMQ6
Entity ID: 2
MoleculeChainsLengthOrganism
crRNAB43Acidaminococcus sp. BV3L6
Entity ID: 3
MoleculeChainsLengthOrganism
Target DNA strandC34Acidaminococcus sp. BV3L6
Entity ID: 4
MoleculeChainsLengthOrganism
Non-target DNA strandD10Acidaminococcus sp. BV3L6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
A, B, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO
Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 80.656α = 90.00
b = 133.298β = 90.00
c = 200.020γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
MOLREPphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-07-26
    Type: Database references