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- EMDB-60476: Cryo-EM structure of the Cas13a-rAcrVIA1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60476
TitleCryo-EM structure of the Cas13a-rAcrVIA1 complex
Map data
Sample
  • Complex: Cas13a-rAcrVIA1 complex
    • Protein or peptide: CRISPR-associated endoribonuclease Cas13a
    • RNA: 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 / CRISPR-associated endoribonuclease Cas13a
Function and homology information
Biological speciesListeria seeligeri serovar 1/2b str. SLCC3954 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsZhang JT / Li YL / Jia N
Funding support1 items
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, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60476.png

Downloads & links

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Map

FileDownload / File: emd_60476.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.021674262 - 2.0858963
Average (Standard dev.)0.00091534393 (±0.021121431)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60476_msk_1.map
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Half map: #2

Fileemd_60476_half_map_1.map
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Half map: #1

Fileemd_60476_half_map_2.map
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Sample components

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Entire : Cas13a-rAcrVIA1 complex

EntireName: Cas13a-rAcrVIA1 complex
Components
  • Complex: Cas13a-rAcrVIA1 complex
    • Protein or peptide: CRISPR-associated endoribonuclease Cas13a
    • RNA: rAcrVIA1

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Supramolecule #1: Cas13a-rAcrVIA1 complex

SupramoleculeName: Cas13a-rAcrVIA1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Listeria seeligeri serovar 1/2b str. SLCC3954 (bacteria)

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Macromolecule #1: CRISPR-associated endoribonuclease Cas13a

MacromoleculeName: CRISPR-associated endoribonuclease Cas13a / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Listeria seeligeri serovar 1/2b str. SLCC3954 (bacteria)
Molecular weightTheoretical: 132.466438 KDa
Recombinant expressionOrganism: Listeria seeligeri (bacteria)
SequenceString: MWISIKTLIH HLGVLFFCDY MYNRREKKII EVKTMRITKV EVDRKKVLIS RDKNGGKLVY ENEMQDNTEQ IMHHKKSSFY KSVVNKTIC RPEQKQMKKL VHGLLQENSQ EKIKVSDVTK LNISNFLNHR FKKSLYYFPE NSPDKSEEYR IEINLSQLLE D SLKKQQGT ...String:
MWISIKTLIH HLGVLFFCDY MYNRREKKII EVKTMRITKV EVDRKKVLIS RDKNGGKLVY ENEMQDNTEQ IMHHKKSSFY KSVVNKTIC RPEQKQMKKL VHGLLQENSQ EKIKVSDVTK LNISNFLNHR FKKSLYYFPE NSPDKSEEYR IEINLSQLLE D SLKKQQGT FICWESFSKD MELYINWAEN YISSKTKLIK KSIRNNRIQS TESRSGQLMD RYMKDILNKN KPFDIQSVSE KY QLEKLTS ALKATFKEAK KNDKEINYKL KSTLQNHERQ IIEELKENSE LNQFNIEIRK HLETYFPIKK TNRKVGDIRN LEI GEIQKI VNHRLKNKIV QRILQEGKLA SYEIESTVNS NSLQKIKIEE AFALKFINAC LFASNNLRNM VYPVCKKDIL MIGE FKNSF KEIKHKKFIR QWSQFFSQEI TVDDIELASW GLRGAIAPIR NEIIHLKKHS WKKFFNNPTF KVKKSKIING KTKDV TSEF LYKETLFKDY FYSELDSVPE LIINKMESSK ILDYYSSDQL NQVFTIPNFE LSLLTSAVPF APSFKRVYLK GFDYQN QDE AQPDYNLKLN IYNEKAFNSE AFQAQYSLFK MVYYQVFLPQ FTTNNDLFKS SVDFILTLNK ERKGYAKAFQ DIRKMNK DE KPSEYMSYIQ SQLMLYQKKQ EEKEKINHFE KFINQVFIKG FNSFIEKNRL TYICHPTKNT VPENDNIEIP FHTDMDDS N IAFWLMCKLL DAKQLSELRN EMIKFSCSLQ STEEISTFTK AREVIGLALL NGEKGCNDWK ELFDDKEAWK KNMSLYVSE ELLQSLPYTQ EDGQTPVINR SIDLVKKYGT ETILEKLFSS SDDYKVSAKD IAKLHEYDVT EKIAQQESLH KQWIEKPGLA RDSAWTKKY QNVINDISNY QWAKTKVELT QVRHLHQLTI DLLSRLAGYM SIADRDFQFS SNYILERENS EYRVTSWILL S ENKNKNKY NDYELYNLKN ASIKVSSKND PQLKVDLKQL RLTLEYLELF DNRLKEKRNN ISHFNYLNGQ LGNSILELFD DA RDVLSYD RKLKNAVSKS LKEILSSHGM EVTFKPLYQT NHHLKIDKLQ PKKIHHLGEK STVSSNQVSN EYCQLVRTLL TMK

UniProtKB: CRISPR-associated endoribonuclease Cas13a

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Macromolecule #2: rAcrVIA1

MacromoleculeName: rAcrVIA1 / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Listeria seeligeri serovar 1/2b str. SLCC3954 (bacteria)
Molecular weightTheoretical: 20.757244 KDa
SequenceString:
UAGCAUCCCA AUAGUGAAGG GAUCUAAAAC UUUUUAUCGC CGGGAUCGCA AGUCCCGGUU UUUUU

GENBANK: GENBANK: CP148897.1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 451586
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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