5XH7 | pdb_00005xh7

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

• PDB DOI: https://doi.org/10.2210/pdb5XH7/pdb
• NAKB: 5XH7

• Classification: HYDROLASE/RNA/DNA
• Organism(s): Acidaminococcus sp. BV3L6
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-04-19 Released: 2017-06-14 
• Deposition Author(s): Nishimasu, H., Yamano, T., Ishitani, R., Nureki, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.214 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

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

• PubMed: 28595896 
• DOI: https://doi.org/10.1016/j.molcel.2017.04.019
• Primary Citation 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 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.

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Organizational Affiliation: 
• Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; JST, PRESTO, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address: [e-mail].
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 180.14 kDa 
• Atom Count: 12,823 
• Modeled Residue Count: 1,363 
• Deposited Residue Count: 1,397 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cpf1	A	1,310	Acidaminococcus sp. BV3L6	Mutation(s): 2  Gene Names: cpf1, HMPREF1246_0236 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 ID: 2
Molecule	Chains	Length	Organism	Image
crRNA	B	43	Acidaminococcus sp. BV3L6

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Target DNA strand	C	34	Acidaminococcus sp. BV3L6

Entity ID: 4
Molecule	Chains	Length	Organism	Image
Non-target DNA strand	D	10	Acidaminococcus sp. BV3L6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], W [auth B], X [auth B], Y [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A], T [auth B], U [auth B], V [auth B], Z [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.214 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.656	α = 90
b = 133.298	β = 90
c = 200.02	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-14 
Deposition Author(s): Nishimasu, H., Yamano, T., Ishitani, R., Nureki, O.

Revision History  

• Version 1.0: 2017-06-14
  Type: Initial release
  
• Version 1.1: 2017-07-26
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description