+Open data
-Basic information
Entry | Database: PDB / ID: 8dex | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | type I-C Cascade | |||||||||
Components |
| |||||||||
Keywords | RNA BINDING PROTEIN/RNA / type I-C / CRISPR / Cascade / DNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding Similarity search - Function | |||||||||
Biological species | Desulfovibrio vulgaris (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | O'Brien, R.E. / Bravo, J.P.K. / Ramos, D. / Hibshman, G.N. / Wright, J.T. / Taylor, D.W. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Mol Cell / Year: 2023 Title: Structural snapshots of R-loop formation by a type I-C CRISPR Cascade. Authors: Roisin E O'Brien / Jack P K Bravo / Delisa Ramos / Grace N Hibshman / Jacquelyn T Wright / David W Taylor / Abstract: Type I CRISPR-Cas systems employ multi-subunit Cascade effector complexes to target foreign nucleic acids for destruction. Here, we present structures of D. vulgaris type I-C Cascade at various ...Type I CRISPR-Cas systems employ multi-subunit Cascade effector complexes to target foreign nucleic acids for destruction. Here, we present structures of D. vulgaris type I-C Cascade at various stages of double-stranded (ds)DNA target capture, revealing mechanisms that underpin PAM recognition and Cascade allosteric activation. We uncover an interesting mechanism of non-target strand (NTS) DNA stabilization via stacking interactions with the "belly" subunits, securing the NTS in place. This "molecular seatbelt" mechanism facilitates efficient R-loop formation and prevents dsDNA reannealing. Additionally, we provide structural insights into how two anti-CRISPR (Acr) proteins utilize distinct strategies to achieve a shared mechanism of type I-C Cascade inhibition by blocking PAM scanning. These observations form a structural basis for directional R-loop formation and reveal how different Acr proteins have converged upon common molecular mechanisms to efficiently shut down CRISPR immunity. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8dex.cif.gz | 1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8dex.ent.gz | 906.9 KB | Display | PDB format |
PDBx/mmJSON format | 8dex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dex_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8dex_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8dex_validation.xml.gz | 82.7 KB | Display | |
Data in CIF | 8dex_validation.cif.gz | 127.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/8dex ftp://data.pdbj.org/pub/pdb/validation_reports/de/8dex | HTTPS FTP |
-Related structure data
Related structure data | 27402MC 8dejC 8dfaC 8dfoC 8dfsC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 25977.857 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) Strain: ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough Gene: DVUA0130 / Production host: Escherichia coli (E. coli) References: UniProt: Q72WF9, Hydrolases; Acting on ester bonds | ||||||
---|---|---|---|---|---|---|---|
#2: Protein | Mass: 32358.912 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) Strain: ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough Gene: DVUA0132 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72WF7 #3: Protein | | Mass: 68123.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) Strain: ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough Gene: DVUA0131 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72WF8 #4: Protein | Mass: 14017.981 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) Strain: ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough Gene: DVUA0131 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72WF8 #5: RNA chain | | Mass: 15476.264 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: Hildenborough / Production host: Escherichia coli (E. coli) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: type I-C Cascade / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Desulfovibrio vulgaris (bacteria) / Strain: Hildenborough |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
---|---|
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 40.5 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73220 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|