8ZTY | pdb_00008zty

Cryo-EM structure of the Cas13a-rAcrVIA1 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

RNA-mediated CRISPR-Cas13 inhibition through crRNA structural mimicry.

Hayes, V.M.Zhang, J.T.Katz, M.A.Li, Y.Kocsis, B.Brinkley, D.M.Jia, N.Meeske, A.J.

(2025) Science 388: 387-391

  • DOI: https://doi.org/10.1126/science.adr3656
  • Primary Citation of Related Structures:  
    8ZTY

  • PubMed Abstract: 

    To circumvent CRISPR-Cas immunity, phages express anti-CRISPR factors that inhibit the expression or activities of Cas proteins. Whereas most anti-CRISPRs described to date are proteins, recently described small RNAs called RNA anti-CRISPRs (rAcrs) have sequence homology to CRISPR RNAs (crRNAs) and displace them from cognate Cas nucleases. In this work, we report the discovery of rAcrVIA1-a plasmid-encoded small RNA that inhibits the RNA-targeting CRISPR-Cas13 system in its natural host, Listeria seeligeri . We solved the cryo-electron microscopy structure of the Cas13-rAcr complex, which revealed that rAcrVIA1 adopts a fold nearly identical to crRNA despite sharing negligible sequence similarity. Collectively, our findings expand the diversity of rAcrs and reveal an example of immune antagonism through RNA structural mimicry.


  • Organizational Affiliation
    • Department of Microbiology, University of Washington, Seattle, WA, USA.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endoribonuclease Cas13a1,120Listeria seeligeri serovar 1/2b str. SLCC3954Mutation(s): 0 
Gene Names: cas13c2c2lse_1149
EC: 3.1
UniProt
Find proteins for P0DPB8 (Listeria seeligeri serovar 1/2b (strain ATCC 35967 / DSM 20751 / CCM 3970 / CCUG 15530 / CIP 100100 / LMG 11386 / NCTC 11856 / SLCC 3954 / 1120))
Explore P0DPB8 
Go to UniProtKB:  P0DPB8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DPB8
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
rAcrVIA165Listeria seeligeri serovar 1/2b str. SLCC3954
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-05-07
    Changes: Data collection, Database references