5B43

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.220 

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

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR-associated endonuclease Cpf1
A
1310Acidaminococcus sp. (strain BV3L6)Mutation(s): 0 
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
RNA (43-MER)B43Acidaminococcus
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (34-MER)C34Acidaminococcus
Entity ID: 4
MoleculeChainsLengthOrganism
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
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 81.515α = 90.00
b = 136.732β = 90.00
c = 196.909γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PHENIXphasing
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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