5B43

Crystal structure of Acidaminococcus sp. Cpf1 in complex with crRNA and target DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA

Yamano, T.Nishimasu, H.Zetsche, B.Hirano, H.Slaymaker, I.M.Li, Y.Fedorova, I.Nakane, T.Makarova, K.S.Koonin, E.V.Ishitani, R.Zhang, F.Nureki, O.

(2016) Cell 165: 949-962

  • DOI: 10.1016/j.cell.2016.04.003
  • Primary Citation of Related Structures:  
    5B43

  • PubMed Abstract: 
  • Cpf1 is an RNA-guided endonuclease of a type V CRISPR-Cas system that has been recently harnessed for genome editing. Here, we report the crystal structure of Acidaminococcus sp. Cpf1 (AsCpf1) in complex with the guide RNA and its target DNA at 2.8 Å ...

    Cpf1 is an RNA-guided endonuclease of a type V CRISPR-Cas system that has been recently harnessed for genome editing. Here, we report the crystal structure of Acidaminococcus sp. Cpf1 (AsCpf1) in complex with the guide RNA and its target DNA at 2.8 Å resolution. AsCpf1 adopts a bilobed architecture, with the RNA-DNA heteroduplex bound inside the central channel. The structural comparison of AsCpf1 with Cas9, a type II CRISPR-Cas nuclease, reveals both striking similarity and major differences, thereby explaining their distinct functionalities. AsCpf1 contains the RuvC domain and a putative novel nuclease domain, which are responsible for cleaving the non-target and target strands, respectively, and for jointly generating staggered DNA double-strand breaks. AsCpf1 recognizes the 5'-TTTN-3' protospacer adjacent motif by base and shape readout mechanisms. Our findings provide mechanistic insights into RNA-guided DNA cleavage by Cpf1 and establish a framework for rational engineering of the CRISPR-Cpf1 toolbox.


    Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 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): 0 
Gene Names: cpf1cas12aHMPREF1246_0236
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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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (43-MER)B43Acidaminococcus
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (34-MER)C34Acidaminococcus
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  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*AP*GP*TP*CP*CP*TP*TP*TP*A)-3')D10Acidaminococcus
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    EDO
    Query on EDO

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

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

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.80 Å
    • R-Value Free: 0.257 
    • R-Value Work: 0.220 
    • R-Value Observed: 0.222 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 81.515α = 90
    b = 136.732β = 90
    c = 196.909γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    Aimlessdata scaling
    PDB_EXTRACTdata extraction
    Cootmodel building
    PHENIXphasing

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2016-05-04
      Type: Initial release
    • Version 1.1: 2016-05-18
      Changes: Database references
    • Version 1.2: 2017-10-04
      Changes: Data collection, Derived calculations