6P7M | pdb_00006p7m

Cryo-EM structure of LbCas12a-crRNA: AcrVA4 (1:2 complex)

• PDB DOI: https://doi.org/10.2210/pdb6P7M/pdb
• EM Map EMD-20266: EMDB EMDataResource
• NAKB: 6P7M

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Lachnospiraceae bacterium ND2006, Moraxella bovoculi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-06-06 Released: 2019-08-21 
• Deposition Author(s): Knott, G.J., Liu, J.J., Doudna, J.A.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a.

Knott, G.J., Cress, B.F., Liu, J.J., Thornton, B.W., Lew, R.J., Al-Shayeb, B., Rosenberg, D.J., Hammel, M., Adler, B.A., Lobba, M.J., Xu, M., Arkin, A.P., Fellmann, C., Doudna, J.A.

(2019) Elife 8

• PubMed: 31397669 
• DOI: https://doi.org/10.7554/eLife.49110
• Primary Citation Related Structures: 
  6P7M, 6P7N


• PubMed Abstract: 
  

  CRISPR-Cas systems provide bacteria and archaea with programmable immunity against mobile genetic elements. Evolutionary pressure by CRISPR-Cas has driven bacteriophage to evolve small protein inhibitors, anti-CRISPRs (Acrs), that block Cas enzyme function by wide-ranging mechanisms. We show here that the inhibitor AcrVA4 uses a previously undescribed strategy to recognize the L. bacterium Cas12a (LbCas12a) pre-crRNA processing nuclease, forming a Cas12a dimer, and allosterically inhibiting DNA binding. The Ac. species Cas12a (AsCas12a) enzyme, widely used for genome editing applications, contains an ancestral helical bundle that blocks AcrVA4 binding and allows it to escape anti-CRISPR recognition. Using biochemical, microbiological, and human cell editing experiments, we show that Cas12a orthologs can be rendered either sensitive or resistant to AcrVA4 through rational structural engineering informed by evolution. Together, these findings explain a new mode of CRISPR-Cas inhibition and illustrate how structural variability in Cas effectors can drive opportunistic co-evolution of inhibitors by bacteriophage.

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Organizational Affiliation: 
• Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.
Gladstone Institutes, San Francisco, United States.
Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States.
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.
Graduate Group in Biophysics, University of California, Berkeley, Berkeley, United States.
UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, United States.
Department of Bioengineering, University of California, Berkeley, Berkeley, United States.
Department of Chemistry, University of California, Berkeley, Berkeley, United States.
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, United States.
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.
Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States.
Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.
California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, SAXS

Macromolecule Content 

• Total Structure Weight: 184.67 kDa 
• Atom Count: 10,141 
• Modeled Residue Count: 1,194 
• Deposited Residue Count: 1,508 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas12a	A	1,231	Lachnospiraceae bacterium ND2006	Mutation(s): 0  Gene Names: lbcas12a
UniProt
Find proteins for A0ACD6BAZ6 (Lachnospiraceae bacterium ND2006) Explore A0ACD6BAZ6  Go to UniProtKB:  A0ACD6BAZ6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-CRISPR VA4	C	237	Moraxella bovoculi	Mutation(s): 0  Gene Names: AAX07_09545

Entity ID: 2
Molecule	Chains	Length	Organism	Image
mature crRNA	B	40	Lachnospiraceae bacterium ND2006

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth B], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-08-21 
Deposition Author(s): Knott, G.J., Liu, J.J., Doudna, J.A.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2019-08-21
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Author supporting evidence
• Version 1.2: 2019-12-18
  Changes: Other
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references