+Open data
-Basic information
Entry | Database: PDB / ID: 8ydb | ||||||
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Title | Type I-FHNH Cascade-dsDNA intermediate complex | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/DNA/RNA / protein / RNA / RNA BINDING PROTEIN-DNA-RNA complex | ||||||
Function / homology | DNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Selenomonas sp. (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: Li, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ydb.cif.gz | 522.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ydb.ent.gz | 428.3 KB | Display | PDB format |
PDBx/mmJSON format | 8ydb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ydb_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8ydb_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8ydb_validation.xml.gz | 82.7 KB | Display | |
Data in CIF | 8ydb_validation.cif.gz | 127.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/8ydb ftp://data.pdbj.org/pub/pdb/validation_reports/yd/8ydb | HTTPS FTP |
-Related structure data
Related structure data | 39167MC 8yb6C 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
-Protein , 4 types, 9 molecules ABIHGFEDJ
#1: Protein | Mass: 28703.135 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Selenomonas sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) | ||
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#2: Protein | Mass: 20735.873 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Selenomonas sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) | ||
#4: Protein | Mass: 38700.172 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Selenomonas sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) #5: Protein | | Mass: 39339.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Selenomonas sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) |
-RNA chain , 1 types, 1 molecules C
#3: RNA chain | Mass: 19440.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Selenomonas sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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-DNA/RNA hybrid , 2 types, 2 molecules TN
#6: DNA/RNA hybrid | Mass: 10086.293 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Selenomonas sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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#7: DNA/RNA hybrid | Mass: 3541.243 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Selenomonas sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) |
-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-FHNH Cascade-dsDNA intermediate complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Selenomonas sp. (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: 1200 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: 88977 / Symmetry type: POINT | ||||||||||||||||||||||||
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