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- EMDB-66731: Cryo-EM structure of csy3 with crRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-66731
TitleCryo-EM structure of csy3 with crRNA
Map data
Sample
  • Complex: Solenoid2
    • Protein or peptide: CRISPR-associated protein Csy3
    • RNA: RNA (159-MER)
KeywordsCRISPR-Cas system / IMMUNE SYSTEM-RNA complex
Function / homologyCRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3) / defense response to virus / CRISPR-associated protein Csy3
Function and homology information
Biological speciesPectobacterium atrosepticum SCRI1043 (bacteria) / Thiocystis violascens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.85 Å
AuthorsGao X / Cui S / Zhu H / Zhu K
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol Cell / Year: 2025
Title: RNA anti-CRISPRs deplete Cas proteins to inhibit the CRISPR-Cas system.
Authors: Xiaopan Gao / Kaixiang Zhu / Weihe Zhang / Lin Wang / Linyue Wang / Lei Hua / Tongxin Niu / Bo Qin / Xia Yu / Hongtao Zhu / Sheng Cui /
Abstract: RNA-based anti-CRISPRs (Racrs) interfere with the type I-F CRISPR-Cas system by mimicking the repeats found in CRISPR arrays. Here, we determined the cryo-electron microscopy (cryo-EM) structures of ...RNA-based anti-CRISPRs (Racrs) interfere with the type I-F CRISPR-Cas system by mimicking the repeats found in CRISPR arrays. Here, we determined the cryo-electron microscopy (cryo-EM) structures of the type I-F crRNA-guided surveillance complex (Csy complex) from Pectobacterium atrosepticum and three RacrIF1-induced aberrant subcomplexes. Additionally, we observed that Cas7f proteins could bind to non-specific nucleic acids, forming right-handed superhelical filaments composed of different Cas7 copies. Mechanistically, RacrIF1 lacks the specific S-conformation observed in the corresponding position of the 5' handle in canonical CRISPR complexes, and it instead adopts a periodic "5 + 1" pattern. This conformation creates severe steric hindrance for Cas5f-Cas8f heterodimer and undermines their binding. Furthermore, Cas7f nonspecifically binds nucleic acids and can form infinite superhelical filaments along Racrs molecules. This oligomerization sequesters Cas6f and Cas7f from binding, therefore blocking the formation of functional CRISPR-Cas effector complexes and ultimately blocking antiviral immunity. Our study provides a structural basis underlying Racrs-mediated CRISPRs inhibition.
History
DepositionOct 25, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66731.png

Downloads & links

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Map

FileDownload / File: emd_66731.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 480 pix.
= 393.6 Å		0.82 Å/pix.
x 480 pix.
= 393.6 Å		0.82 Å/pix.
x 480 pix.
= 393.6 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.0037533483 - 1.8268344
Average (Standard dev.)0.0037020342 (±0.04286997)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 393.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66731_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66731_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Solenoid2

EntireName: Solenoid2
Components
  • Complex: Solenoid2
    • Protein or peptide: CRISPR-associated protein Csy3
    • RNA: RNA (159-MER)

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Supramolecule #1: Solenoid2

SupramoleculeName: Solenoid2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pectobacterium atrosepticum SCRI1043 (bacteria)

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Macromolecule #1: CRISPR-associated protein Csy3

MacromoleculeName: CRISPR-associated protein Csy3 / type: protein_or_peptide / ID: 1 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Pectobacterium atrosepticum SCRI1043 (bacteria)
Molecular weightTheoretical: 36.948512 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAKAATTLKT ASVLAFERKL ANSDALMYAG NWAQQDNWTA IAIQEKSVRG TISNRLKNAL TSDPAKLDAE IQKANLQKVD VAALPFGAD TLKIVFTLRV LGNLAQPSVC NDQDYQTALG DIITGYAQEQ GFSTLAARYA ENIANGRFLW RNRVGAEAIR V VVTKKGER ...String:
MAKAATTLKT ASVLAFERKL ANSDALMYAG NWAQQDNWTA IAIQEKSVRG TISNRLKNAL TSDPAKLDAE IQKANLQKVD VAALPFGAD TLKIVFTLRV LGNLAQPSVC NDQDYQTALG DIITGYAQEQ GFSTLAARYA ENIANGRFLW RNRVGAEAIR V VVTKKGER SWEFNGEDYS LRQFSQPAGD LAALTQAIEK GLAGDASALF TVEAYVQLGN GQEVFPSQEL VLDEKARNGK SK ILYQVND VAAIHSQKIG NALRTIDDWY PAADEAGPIA VEPYGSVTSR GKAYRQPREK MDFYTLLDNW VIKGDVPMPE QQH YVIATL IRGGVFGEKG E

UniProtKB: CRISPR-associated protein Csy3

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Macromolecule #2: RNA (159-MER)

MacromoleculeName: RNA (159-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Thiocystis violascens (bacteria)
Molecular weightTheoretical: 51.550691 KDa
SequenceString:
ACGGCGAAAG CGGGCUUGAA AUUCACGGCG AAAUUCACGG CGGGCUUGAA AUUCACGGCG GGAUUCACGG CGGGCUUGAA AUUCACGGC GAAAUUCACG GCGGGCUUGA AAUUCACGGC GAAAUUCACG GCGGGCUUGA AAUUCACGGC GGGAUUCACG

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 140643
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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