Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 178.19 kDa 
• Atom Count: 12,319 
• Modelled Residue Count: 1,224 
• Deposited Residue Count: 1,224 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

 7VW3

Cryo-EM structure of SaCas9-sgRNA-DNA ternary complex

• PDB DOI: 10.2210/pdb7VW3/pdb
• EM Map EMD-32104: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN/RNA/DNA
• Organism(s): Staphylococcus aureus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-11-09 Released: 2023-03-15 
• Deposition Author(s): Du, W.H., Qian, J.Q., Huang, Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Full-Length Model of SaCas9-sgRNA-DNA Complex in Cleavage State.

Du, W., Zhu, H., Qian, J., Xue, D., Zheng, S., Huang, Q.

(2023) Int J Mol Sci 24

• PubMed: 36674715 
• DOI: 10.3390/ijms24021204
• Primary Citation of Related Structures:  
  7VW3


• PubMed Abstract: 
  

Staphylococcus aureus Cas9 (SaCas9) is a widely used genome editing tool. Understanding its molecular mechanisms of DNA cleavage could effectively guide the engineering optimization of this system. Here, we determined the first cryo-electron microscopy structure of the SaCas9-sgRNA-DNA ternary complex. This structure reveals that the HNH nuclease domain is tightly bound to the cleavage site of the target DNA strand, and is in close contact with the WED and REC domains. Moreover, it captures the complete structure of the sgRNA, including the previously unresolved stem-loop 2. Based on this structure, we build a full-length model for the ternary complex in cleavage state. This model enables identification of the residues for the interactions between the HNH domain and the WED and REC domains. Moreover, we found that the stem-loop 2 of the sgRNA tightly binds to the PI and RuvC domains and may also regulate the position shift of the RuvC domain. Further mutagenesis and molecular dynamics simulations supported the idea that the interactions of the HNH domain with the WED and REC domains play an important role in the DNA cleavage. Thus, this study provides new mechanistic insights into the DNA cleavage of SaCas9 and is also useful for guiding the future engineering of SaCas9-mediated gene editing systems.

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Organizational Affiliation: 

Multiscale Research Institute for Complex Systems, Fudan University, Shanghai 201203, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas9	A	1,052	Staphylococcus aureus	Mutation(s): 2  Gene Names: cas9 EC: 3.1
UniProt
Find proteins for J7RUA5 (Staphylococcus aureus) Explore J7RUA5  Go to UniProtKB:  J7RUA5

Entity ID: 2
Molecule	Chains	Length	Organism	Image
single-guide RNA	B	104	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Target DNA strand	C	40	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
Non-target DNA strand	D	28	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0.8
MODEL REFINEMENT	PHENIX	1.19.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-15 
Deposition Author(s): Du, W.H., Qian, J.Q., Huang, Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31971377
National Natural Science Foundation of China (NSFC)	China	31671386

Revision History  

• Version 1.0: 2023-03-15
  Type: Initial release