6P7M

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

Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • DOI: https://doi.org/10.7554/eLife.49110
  • Primary Citation of 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 ...

    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.

    Related Citations: 
    • PHENIX: a comprehensive Python-based system for macromolecular structure solution.
      Adams, P.D., Afonine, P.V., Bunkoczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J., Grosse-Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Oeffner, R., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C., Zwart, P.H.
      (2010) Acta Crystallogr D Biol Crystallogr 66: 213
    Organizational Affiliation: 

    California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, United States.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cas12aA1,231Lachnospiraceae bacterium ND2006Mutation(s): 0 
Gene Names: lbcas12a
UniProt
Find proteins for A0A182DWE3 (Lachnospiraceae bacterium ND2006)
Explore A0A182DWE3 
Go to UniProtKB:  A0A182DWE3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A182DWE3
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
anti-CRISPR VA4C237Moraxella bovoculiMutation(s): 0 
Gene Names: AAX07_09545
UniProt
Find proteins for A0A0U2APF4 (Moraxella bovoculi)
Explore A0A0U2APF4 
Go to UniProtKB:  A0A0U2APF4
Entity Groups  
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UniProt GroupA0A0U2APF4
Protein Feature View
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Entity ID: 2
MoleculeChainsLengthOrganismImage
mature crRNAB40Lachnospiraceae bacterium ND2006
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth B],
E [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • 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