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 

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This is version 1.3 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: https://doi.org/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 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cpf11,310Acidaminococcus sp. BV3L6Mutation(s): 0 
Gene Names: cpf1
EC: 3.1 (PDB Primary Data), 4.6.1.22 (UniProt), 3.1.21.1 (UniProt)
UniProt
Find proteins for U2UMQ6 (Acidaminococcus sp. (strain BV3L6))
Explore U2UMQ6 
Go to UniProtKB:  U2UMQ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU2UMQ6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (43-MER)43Acidaminococcus
Sequence Annotations
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (34-MER)34Acidaminococcus
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*AP*GP*TP*CP*CP*TP*TP*TP*A)-3')10Acidaminococcus
Sequence Annotations
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  • Reference Sequence
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  (Full details and data files)

  • 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
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references