6P7N

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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. 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.


  • Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
anti-CRISPR VA4A [auth C],
B [auth G]
237Moraxella bovoculiMutation(s): 0 
Gene Names: AAX07_09545
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cas12aC [auth A],
D [auth E]
1,231Lachnospiraceae 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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
mature crRNAE [auth B],
F
40Lachnospiraceae bacterium ND2006
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 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
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Other