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Crystal structure of Lachnospiraceae bacterium ND2006 Cpf1 in complex with crRNA and target DNA (TCCA PAM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1.

Yamano, T.Zetsche, B.Ishitani, R.Zhang, F.Nishimasu, H.Nureki, O.

(2017) Mol. Cell 67: 633-645.e3

  • DOI: 10.1016/j.molcel.2017.06.035
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The RNA-guided Cpf1 (also known as Cas12a) nuclease associates with a CRISPR RNA (crRNA) and cleaves the double-stranded DNA target complementary to the crRNA guide. The two Cpf1 orthologs from Acidaminococcus sp. (AsCpf1) and Lachnospiraceae bacteri ...

    The RNA-guided Cpf1 (also known as Cas12a) nuclease associates with a CRISPR RNA (crRNA) and cleaves the double-stranded DNA target complementary to the crRNA guide. The two Cpf1 orthologs from Acidaminococcus sp. (AsCpf1) and Lachnospiraceae bacterium (LbCpf1) have been harnessed for eukaryotic genome editing. Cpf1 requires a specific nucleotide sequence, called a protospacer adjacent motif (PAM), for target recognition. Besides the canonical TTTV PAM, Cpf1 recognizes suboptimal C-containing PAMs. Here, we report four crystal structures of LbCpf1 in complex with the crRNA and its target DNA containing either TTTA, TCTA, TCCA, or CCCA as the PAM. These structures revealed that, depending on the PAM sequences, LbCpf1 undergoes conformational changes to form altered interactions with the PAM-containing DNA duplexes, thereby achieving the relaxed PAM recognition. Collectively, the present structures advance our mechanistic understanding of the PAM-dependent, crRNA-guided DNA cleavage by the Cpf1 family nucleases.


    Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LbCpf1
A
1231Lachnospiraceae bacterium ND2006Mutation(s): 0 
Find proteins for A0A182DWE3 (Lachnospiraceae bacterium ND2006)
Go to UniProtKB:  A0A182DWE3
Entity ID: 2
MoleculeChainsLengthOrganism
crRNAB40synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (29-MER)C29synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*TP*CP*CP*TP*CP*CP*A)-3')D9synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
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
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.193 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 101.954α = 90.00
b = 101.954β = 90.00
c = 372.544γ = 90.00
Software Package:
Software NamePurpose
DIALSdata reduction
Aimlessdata scaling
PHENIXrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Database references