6NY2 | pdb_00006ny2

CasX-gRNA-DNA(45bp) state I

• PDB DOI: https://doi.org/10.2210/pdb6NY2/pdb
• Entry: 6NY2 supersedes: 6E79
• NAKB: 6NY2
• EM Map EMD-8996: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN/RNA/DNA
• Organism(s): Deltaproteobacteria bacterium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-02-10 Released: 2019-02-27 
• Deposition Author(s): Liu, J.J., Orlova, N., Nogales, E., Doudna, J.A.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

CasX enzymes comprise a distinct family of RNA-guided genome editors.

Liu, J.J., Orlova, N., Oakes, B.L., Ma, E., Spinner, H.B., Baney, K.L.M., Chuck, J., Tan, D., Knott, G.J., Harrington, L.B., Al-Shayeb, B., Wagner, A., Brotzmann, J., Staahl, B.T., Taylor, K.L., Desmarais, J., Nogales, E., Doudna, J.A.

(2019) Nature 566: 218-223

• PubMed: 30718774 
• DOI: https://doi.org/10.1038/s41586-019-0908-x
• Primary Citation of Related Structures:  
  6NY1, 6NY2, 6NY3


• PubMed Abstract: 
  

  The RNA-guided CRISPR-associated (Cas) proteins Cas9 and Cas12a provide adaptive immunity against invading nucleic acids, and function as powerful tools for genome editing in a wide range of organisms. Here we reveal the underlying mechanisms of a third, fundamentally distinct RNA-guided genome-editing platform named CRISPR-CasX, which uses unique structures for programmable double-stranded DNA binding and cleavage. Biochemical and in vivo data demonstrate that CasX is active for Escherichia coli and human genome modification. Eight cryo-electron microscopy structures of CasX in different states of assembly with its guide RNA and double-stranded DNA substrates reveal an extensive RNA scaffold and a domain required for DNA unwinding. These data demonstrate how CasX activity arose through convergent evolution to establish an enzyme family that is functionally separate from both Cas9 and Cas12a.

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Organizational Affiliation: 
• Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Clayton Foundation Laboratories of Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.
Department of Plant and Microbiology, University of California, Berkeley, CA, USA.
Max-Planck-Institute for Biochemistry, Planegg, Germany.
Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-University, Munich, Germany.
Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA. [e-mail].
California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA. [e-mail].
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [e-mail].
Howard Hughes Medical Institute, University of California, Berkeley, CA, USA. [e-mail].
Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA. [e-mail].
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [e-mail].
Innovative Genomics Institute, University of California, Berkeley, CA, USA. [e-mail].
Howard Hughes Medical Institute, University of California, Berkeley, CA, USA. [e-mail].
Department of Chemistry, University of California, Berkeley, CA, USA. [e-mail].
Gladstone Institutes, San Francisco, CA, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: cross-linking

Macromolecule Content 

• Total Structure Weight: 174.93 kDa 
• Atom Count: 10,538 
• Modeled Residue Count: 1,095 
• Deposited Residue Count: 1,198 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CasX	C [auth Y]	986	Deltaproteobacteria bacterium	Mutation(s): 0  Gene Names: DD725_10130

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA target strand	A [auth C]	45	Deltaproteobacteria bacterium

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA Non-target strand	B [auth D]	45	Deltaproteobacteria bacterium

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (110-MER)	D [auth B]	122	Deltaproteobacteria bacterium

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-02-27 
Deposition Author(s): Liu, J.J., Orlova, N., Nogales, E., Doudna, J.A.
• This entry supersedes: 6E79

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	p01

Revision History  

• Version 1.0: 2019-02-27
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2019-12-25
  Changes: Database references
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Structure summary