+Open data
-Basic information
Entry | Database: PDB / ID: 8yha | ||||||
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Title | Type I-EHNH Cascade-ssDNA complex | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/DNA/RNA / protein / RNA BINDING PROTEIN-DNA-RNA complex | ||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria) Candidatus Cloacimonadota bacterium (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Li, Z. | ||||||
Funding support | 1items
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Citation | Journal: Mol Cell / Year: 2024 Title: Mechanisms for HNH-mediated target DNA cleavage in type I CRISPR-Cas systems. Authors: Chendi Zhang / Fugen Chen / Feng Wang / Haijiang Xu / Jialin Xue / Zhuang Li / Abstract: The metagenome-derived type I-E and type I-F variant CRISPR-associated complex for antiviral defense (Cascade) complexes, fused with HNH domains, precisely cleave target DNA, representing recently ...The metagenome-derived type I-E and type I-F variant CRISPR-associated complex for antiviral defense (Cascade) complexes, fused with HNH domains, precisely cleave target DNA, representing recently identified genome editing tools. However, the underlying working mechanisms remain unknown. Here, structures of type I-F and I-E Cascade complexes at different states are reported. In type I-F Cascade, Cas8f loosely attaches to Cascade head and is adjacent to the 5' end of the target single-stranded DNA (ssDNA). Formation of the full R-loop drives the Cascade head to move outward, allowing Cas8f to detach and rotate ∼150° to accommodate target ssDNA for cleavage. In type I-E Cascade, Cas5e domain is adjacent to the 5' end of the target ssDNA. Full crRNA-target pairing drives the lift of the Cascade head, widening the substrate channel for target ssDNA entrance. Altogether, these analyses into both complexes revealed that crRNA-guided positioning of target DNA and target DNA-induced HNH unlocking are two key factors for their site-specific cleavage of target DNA. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8yha.cif.gz | 628.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yha.ent.gz | 512.1 KB | Display | PDB format |
PDBx/mmJSON format | 8yha.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8yha_validation.pdf.gz | 442.8 KB | Display | wwPDB validaton report |
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Full document | 8yha_full_validation.pdf.gz | 480.4 KB | Display | |
Data in XML | 8yha_validation.xml.gz | 64 KB | Display | |
Data in CIF | 8yha_validation.cif.gz | 100.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/8yha ftp://data.pdbj.org/pub/pdb/validation_reports/yh/8yha | HTTPS FTP |
-Related structure data
Related structure data | 39286MC 8yb6C 8ydbC 8yeoC 8yh9C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-CRISPR system Cascade subunit ... , 2 types, 7 molecules ADEFGHI
#1: Protein | Mass: 43621.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria) Gene: casD, BWX75_00750 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1V6F8C5 |
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#4: Protein | Mass: 41794.367 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria) Gene: casC, BWX75_00749 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1V6F8B5 |
-CRISPR-associated protein ... , 2 types, 2 molecules JK
#5: Protein | Mass: 60665.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria) Gene: BWX75_00747 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1V6F8D1 |
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#6: Protein | Mass: 20300.639 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria) Gene: BWX75_00748 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1V6F8C9 |
-Protein / RNA chain / DNA/RNA hybrid / Non-polymers , 4 types, 5 molecules BCT
#2: Protein | Mass: 31218.768 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria) Gene: cse3, BWX75_00751 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A1V6F8C4, Hydrolases; Acting on ester bonds |
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#3: RNA chain | Mass: 19681.744 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Cloacimonadota bacterium (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) |
#7: DNA/RNA hybrid | Mass: 17561.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Cloacimonadota bacterium (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) |
#8: Chemical |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Type I-EHNH Cascade-ssDNA complex / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT |
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Source (natural) | Organism: Candidatus Cloacimonadota bacterium (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63162 / Symmetry type: POINT | ||||||||||||||||||||||||
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