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- PDB-8zty: Cryo-EM structure of the Cas13a-rAcrVIA1 complex -

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Basic information

Entry
Database: PDB / ID: 8zty
TitleCryo-EM structure of the Cas13a-rAcrVIA1 complex
Components
  • CRISPR-associated endoribonuclease Cas13a
  • rAcrVIA1
KeywordsRNA BINDING PROTEIN/RNA / STRUCTURAL PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology: / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding / : / RNA / RNA (> 10) / CRISPR-associated endoribonuclease Cas13a
Function and homology information
Biological speciesListeria seeligeri serovar 1/2b str. SLCC3954 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsZhang, J.T. / Li, Y.L. / Jia, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Science / Year: 2025
Title: RNA-mediated CRISPR-Cas13 inhibition through crRNA structural mimicry.
Authors: Victoria M Hayes / Jun-Tao Zhang / Mark A Katz / Yuelong Li / Benjamin Kocsis / David M Brinkley / Ning Jia / Alexander J Meeske /
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 ...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, . 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.
History
DepositionJun 7, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated endoribonuclease Cas13a
B: rAcrVIA1


Theoretical massNumber of molelcules
Total (without water)153,2242
Polymers153,2242
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein CRISPR-associated endoribonuclease Cas13a / CRISPR-associated endoribonuclease C2c2 / EndoRNase / LseC2c2


Mass: 132466.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria seeligeri serovar 1/2b str. SLCC3954 (bacteria)
Gene: cas13, c2c2, lse_1149 / Production host: Listeria seeligeri (bacteria)
References: UniProt: P0DPB8, Hydrolases; Acting on ester bonds
#2: RNA chain rAcrVIA1


Mass: 20757.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria seeligeri serovar 1/2b str. SLCC3954 (bacteria)
Production host: Listeria seeligeri (bacteria) / References: GenBank: 2703972415
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cas13a-rAcrVIA1 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Listeria seeligeri serovar 1/2b str. SLCC3954 (bacteria)
Source (recombinant)Organism: Listeria seeligeri (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / C2 aperture diameter: 70 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 451586 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039204
ELECTRON MICROSCOPYf_angle_d0.67712642
ELECTRON MICROSCOPYf_dihedral_angle_d14.2461667
ELECTRON MICROSCOPYf_chiral_restr0.0381439
ELECTRON MICROSCOPYf_plane_restr0.0051389

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