5XH6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

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:  
    5XH6, 5XH7

  • 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. Electronic address: nureki@bs.s.u-tokyo.ac.jp.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cpf1A1310Acidaminococcus sp. BV3L6Mutation(s): 3 
Gene Names: cpf1HMPREF1246_0236cas12a
EC: 3.1 (PDB Primary Data), 3.1.21.1 (UniProt), 4.6.1.22 (UniProt)
Find proteins for U2UMQ6 (Acidaminococcus sp. (strain BV3L6))
Explore U2UMQ6 
Go to UniProtKB:  U2UMQ6
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
crRNAB43Acidaminococcus sp. BV3L6
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
Target DNA strandC34Acidaminococcus sp. BV3L6
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    Non-target DNA strandD10Acidaminococcus sp. BV3L6
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    EDO
    Query on EDO

    Download CCD File 
    A, B, C
    1,2-ETHANEDIOL
    C2 H6 O2
    LYCAIKOWRPUZTN-UHFFFAOYSA-N
     Ligand Interaction
    CL
    Query on CL

    Download CCD File 
    A
    CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M
     Ligand Interaction
    NA
    Query on NA

    Download CCD File 
    A, B, C
    SODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.00 Å
    • R-Value Free: 0.210 
    • R-Value Work: 0.175 
    • R-Value Observed: 0.177 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 81.162α = 90
    b = 133.676β = 90
    c = 199.633γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    DIALSdata reduction
    Aimlessdata scaling
    MOLREPphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

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