7M5O | pdb_00007m5o

Cryo-EM structure of CasPhi-2 (Cas12j) bound to crRNA

• PDB DOI: https://doi.org/10.2210/pdb7M5O/pdb
• NAKB: 7M5O
• EM Map EMD-23678: EMDB EMDataResource

• Classification: VIRAL PROTEIN/RNA
• Organism(s): Biggievirus Mos11, Phage #D
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-03-24 Released: 2021-08-04 
• Deposition Author(s): Pausch, P., Soczek, K., Nogales, E., Doudna, J.
• Funding Organization(s): National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.54 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

DNA interference states of the hypercompact CRISPR-Cas Phi effector.

Pausch, P., Soczek, K.M., Herbst, D.A., Tsuchida, C.A., Al-Shayeb, B., Banfield, J.F., Nogales, E., Doudna, J.A.

(2021) Nat Struct Mol Biol 28: 652-661

• PubMed: 34381246 
• DOI: https://doi.org/10.1038/s41594-021-00632-3
• Primary Citation Related Structures: 
  7LYS, 7LYT, 7M5O


• PubMed Abstract: 
  

  CRISPR-CasΦ, a small RNA-guided enzyme found uniquely in bacteriophages, achieves programmable DNA cutting as well as genome editing. To investigate how the hypercompact enzyme recognizes and cleaves double-stranded DNA, we determined cryo-EM structures of CasΦ (Cas12j) in pre- and post-DNA-binding states. The structures reveal a streamlined protein architecture that tightly encircles the CRISPR RNA and DNA target to capture, unwind and cleave DNA. Comparison of the pre- and post-DNA-binding states reveals how the protein rearranges for DNA cleavage upon target recognition. On the basis of these structures, we created and tested mutant forms of CasΦ that cut DNA up to 20-fold faster relative to wild type, showing how this system may be naturally attenuated to improve the fidelity of DNA interference. The structural and mechanistic insights into how CasΦ binds and cleaves DNA should allow for protein engineering for both in vitro diagnostics and genome editing.

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Organizational Affiliation: 
• Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.
VU LSC-EMBL Partnership for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA.
Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA.
Howard Hughes Medical Institute, Baltimore, MD, USA.
Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA. [e-mail].
Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. [e-mail].
California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA. [e-mail].
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [e-mail].
Howard Hughes Medical Institute, Baltimore, MD, USA. [e-mail].
Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA. [e-mail].
Gladstone Institute of Data Science and Biotechnology, 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: gel filtration

Macromolecule Content 

• Total Structure Weight: 100.67 kDa 
• Atom Count: 6,013 
• Modeled Residue Count: 692 
• Deposited Residue Count: 808 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CasPhi	A	763	Biggievirus Mos11	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
crRNA	B	45	Phage #D

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.54 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-08-04 
Deposition Author(s): Pausch, P., Soczek, K., Nogales, E., Doudna, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)	United States	U01AI142817-02

Revision History  

• Version 1.0: 2021-08-04
  Type: Initial release
  
• Version 1.1: 2021-08-25
  Changes: Database references
• Version 1.2: 2024-05-29
  Changes: Data collection