+Open data
-Basic information
Entry | Database: PDB / ID: 8yb6 | ||||||
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Title | Type I-EHNH Cascade complex | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / RNA pro / 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 / hydrolase activity / RNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 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: Li, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8yb6.cif.gz | 684.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yb6.ent.gz | 557.5 KB | Display | PDB format |
PDBx/mmJSON format | 8yb6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8yb6_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8yb6_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8yb6_validation.xml.gz | 99.7 KB | Display | |
Data in CIF | 8yb6_validation.cif.gz | 153.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/8yb6 ftp://data.pdbj.org/pub/pdb/validation_reports/yb/8yb6 | HTTPS FTP |
-Related structure data
Related structure data | 39110MC 8ydbC 8yeoC 8yh9C 8yhaC 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 / Non-polymers , 3 types, 4 molecules BC
#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 Cloacimonetes bacterium ADurb.Bin088 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) |
#7: 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 complex / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT |
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Source (natural) | Organism: Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 6.2 |
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: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 291872 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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