6K57

Crystal structure of dCas9 in complex with sgRNA and DNA (CGA PAM)

• PDB DOI:  https://doi.org/10.2210/pdb6K57/pdb
• NAKB: 6K57

• Classification: HYDROLASE/RNA/DNA
• Organism(s): Streptococcus pyogenes, Streptococcus pyogenes serotype M1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-05-28 Released: 2019-09-25 
• Deposition Author(s): Chen, W., Zhang, H., Zhang, Y., Wang, Y., Gan, J., Ji, Q.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 0.274 
• R-Value Work: 0.197 
• R-Value Observed: 0.201 

Literature

Molecular basis for the PAM expansion and fidelity enhancement of an evolved Cas9 nuclease.

Chen, W., Zhang, H., Zhang, Y., Wang, Y., Gan, J., Ji, Q.

(2019) PLoS Biol 17: e3000496-e3000496

• PubMed: 31603896 
• DOI: https://doi.org/10.1371/journal.pbio.3000496
• Primary Citation of Related Structures:  
  6K3Z, 6K4P, 6K4Q, 6K4S, 6K4U, 6K57


• PubMed Abstract: 
  

Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have been harnessed as powerful genome editing tools in diverse organisms. However, the off-target effects and the protospacer adjacent motif (PAM) compatibility restrict the therapeutic applications of these systems. Recently, a Streptococcus pyogenes Cas9 (SpCas9) variant, xCas9, was evolved to possess both broad PAM compatibility and high DNA fidelity. Through determination of multiple xCas9 structures, which are all in complex with single-guide RNA (sgRNA) and double-stranded DNA containing different PAM sequences (TGG, CGG, TGA, and TGC), we decipher the molecular mechanisms of the PAM expansion and fidelity enhancement of xCas9. xCas9 follows a unique two-mode PAM recognition mechanism. For non-NGG PAM recognition, xCas9 triggers a notable structural rearrangement in the DNA recognition domains and a rotation in the key PAM-interacting residue R1335; such mechanism has not been observed in the wild-type (WT) SpCas9. For NGG PAM recognition, xCas9 applies a strategy similar to WT SpCas9. Moreover, biochemical and cell-based genome editing experiments pinpointed the critical roles of the E1219V mutation for PAM expansion and the R324L, S409I, and M694I mutations for fidelity enhancement. The molecular-level characterizations of the xCas9 nuclease provide critical insights into the mechanisms of the PAM expansion and fidelity enhancement of xCas9 and could further facilitate the engineering of SpCas9 and other Cas9 orthologs.

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Organizational Affiliation: 

School of Physical Science and Technology, ShanghaiTech University, Shanghai, China.

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: 197.66 kDa 
• Atom Count: 13,302 
• Modelled Residue Count: 1,435 
• Deposited Residue Count: 1,491 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas9	B	1,368	Streptococcus pyogenes serotype M1	Mutation(s): 2  Gene Names: cas9, csn1, SPy_1046 EC: 3.1
UniProt
Find proteins for Q99ZW2 (Streptococcus pyogenes serotype M1) Explore Q99ZW2  Go to UniProtKB:  Q99ZW2

Entity ID: 1
Molecule	Chains	Length	Organism	Image
sgRNA	A	83	Streptococcus pyogenes

Entity ID: 3
Molecule	Chains	Length	Organism	Image
target DNA	C	28	Streptococcus pyogenes

Entity ID: 4
Molecule	Chains	Length	Organism	Image
non-target DNA	D	12	Streptococcus pyogenes

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 0.274 
• R-Value Work: 0.197 
• R-Value Observed: 0.201 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.956	α = 90
b = 69.137	β = 110.34
c = 189.243	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PHASER	phasing
HKL-3000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-25 
Deposition Author(s): Chen, W., Zhang, H., Zhang, Y., Wang, Y., Gan, J., Ji, Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	91753127

Revision History  

• Version 1.0: 2019-09-25
  Type: Initial release
  
• Version 1.1: 2019-11-13
  Changes: Database references