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- PDB-9irg: Cryo-EM Structure of RNA -

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Basic information

Entry
Database: PDB / ID: 9irg
TitleCryo-EM Structure of RNA
Components
  • CRISPR-associated protein Csy3
  • RNA (162-MER)
KeywordsRNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA complex
Function / homologyCRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3) / defense response to virus / RNA / RNA (> 10) / RNA (> 100) / CRISPR-associated protein Csy3
Function and homology information
Biological speciesPectobacterium atrosepticum SCRI1043 (bacteria)
Thiocystis violascens (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.59 Å
AuthorsGao, X. / Cui, S. / Zhu, H. / Zhu, K. / Shang, K.
Funding support1items
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
DepositionJul 16, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated protein Csy3
C: CRISPR-associated protein Csy3
D: CRISPR-associated protein Csy3
E: CRISPR-associated protein Csy3
F: CRISPR-associated protein Csy3
G: CRISPR-associated protein Csy3
I: CRISPR-associated protein Csy3
J: CRISPR-associated protein Csy3
K: CRISPR-associated protein Csy3
L: CRISPR-associated protein Csy3
M: RNA (162-MER)
B: CRISPR-associated protein Csy3
H: CRISPR-associated protein Csy3
N: CRISPR-associated protein Csy3
O: CRISPR-associated protein Csy3
P: CRISPR-associated protein Csy3
Q: CRISPR-associated protein Csy3
S: CRISPR-associated protein Csy3
T: CRISPR-associated protein Csy3
U: CRISPR-associated protein Csy3
V: CRISPR-associated protein Csy3
W: CRISPR-associated protein Csy3
Y: CRISPR-associated protein Csy3
Z: CRISPR-associated protein Csy3
a: CRISPR-associated protein Csy3
b: CRISPR-associated protein Csy3
f: CRISPR-associated protein Csy3


Theoretical massNumber of molelcules
Total (without water)1,013,13827
Polymers1,013,13827
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 protein Csy3


Mass: 36948.512 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum SCRI1043 (bacteria)
Gene: csy3, ECA3683 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6D0W6
#2: RNA chain RNA (162-MER)


Mass: 52476.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiocystis violascens (bacteria) / Production host: Escherichia coli (E. coli)
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: complex of RNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Pectobacterium atrosepticum SCRI1043 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 2500 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1800 nm / Calibrated defocus max: 2500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.13_2998model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 4.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9887 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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