6O0X

Conformational states of Cas9-sgRNA-DNA ternary complex in the presence of magnesium

• PDB DOI:  https://doi.org/10.2210/pdb6O0X/pdb
• EM Map EMD-0583: EMDB EMDataResource
• NAKB: 6O0X

• Classification: HYDROLASE/RNA/DNA
• Organism(s): Streptococcus pyogenes, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-02-17 Released: 2019-07-10 
• Deposition Author(s): Zhu, X., Clarke, R., Puppala, A.K., Chittori, S., Merk, A., Merrill, B.J., Simonovic, M., Subramaniam, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.28 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structures reveal coordinated domain motions that govern DNA cleavage by Cas9.

Zhu, X., Clarke, R., Puppala, A.K., Chittori, S., Merk, A., Merrill, B.J., Simonovic, M., Subramaniam, S.

(2019) Nat Struct Mol Biol 26: 679-685

• PubMed: 31285607 
• DOI: https://doi.org/10.1038/s41594-019-0258-2
• Primary Citation of Related Structures:  
  6O0X, 6O0Y, 6O0Z


• PubMed Abstract: 
  

The RNA-guided Cas9 endonuclease from Streptococcus pyogenes is a single-turnover enzyme that displays a stable product state after double-stranded-DNA cleavage. Here, we present cryo-EM structures of precatalytic, postcatalytic and product states of the active Cas9-sgRNA-DNA complex in the presence of Mg ²⁺ . In the precatalytic state, Cas9 adopts the 'checkpoint' conformation with the HNH nuclease domain positioned far away from the DNA. Transition to the postcatalytic state involves a dramatic ~34-Å swing of the HNH domain and disorder of the REC2 recognition domain. The postcatalytic state captures the cleaved substrate bound to the catalytically competent HNH active site. In the product state, the HNH domain is disordered, REC2 returns to the precatalytic conformation, and additional interactions of REC3 and RuvC with nucleic acids are formed. The coupled domain motions and interactions between the enzyme and the RNA-DNA hybrid provide new insights into the mechanism of genome editing by Cas9.

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Organizational Affiliation: 

Frederick National Laboratory for Cancer Research, Frederick, MD, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 216.63 kDa 
• Atom Count: 11,257 
• Modelled Residue Count: 1,262 
• Deposited Residue Count: 1,554 
• Unique protein chains: 1
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas9/Csn1	A	1,372	Streptococcus pyogenes	Mutation(s): 0  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: 2
Molecule	Chains	Length	Organism	Image
single guide RNA	B	102	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5' product of target strand DNA	C	13	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
non-target strand DNA	D	40	synthetic construct

Entity ID: 5
Molecule	Chains	Length	Organism	Image
3' product of target strand DNA	E [auth c]	27	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.28 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Zhu, X., Clarke, R., Puppala, A.K., Chittori, S., Merk, A., Merrill, B.J., Simonovic, M., Subramaniam, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	097042
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	081534
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2019-07-10
  Type: Initial release
  
• Version 1.1: 2019-07-24
  Changes: Data collection, Database references
• Version 1.2: 2019-08-21
  Changes: Data collection, Database references
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 1.4: 2019-12-18
  Changes: Other