6P7N

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.9 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: 10.7554/eLife.49110
  • Primary Citation of Related Structures:  

  • 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 fu ...

    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 A. 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.,Sect.D 66: 213


    Organizational Affiliation

    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Chemistry, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Department of Bioengineering, University of California, Berkeley, Berkeley, United States.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States.,Gladstone Institutes, University of California, San Francisco, San Francisco, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
anti-CRISPR VA4
C, G
237Moraxella bovoculiMutation(s): 0 
Find proteins for A0A0U2APF4 (Moraxella bovoculi)
Go to UniProtKB:  A0A0U2APF4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cas12a
A, E
1231Lachnospiraceae bacterium ND2006Mutation(s): 0 
Find proteins for A0A182DWE3 (Lachnospiraceae bacterium ND2006)
Go to UniProtKB:  A0A182DWE3
Entity ID: 3
MoleculeChainsLengthOrganism
mature crRNAB,F40Lachnospiraceae bacterium ND2006
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement
phenix.real_space_refinerefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant 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
    Type: Author supporting evidence
  • Version 1.2: 2019-12-18
    Type: Other