+Open data
-Basic information
Entry | Database: PDB / ID: 8k87 | ||||||
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Title | Dimer structure of procaryotic Ago | ||||||
Components |
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Keywords | DNA/RNA/CELL INVASION / Ago / DNA/RNA / DNA BINDING PROTEIN / CELL INVASION / DNA-RNA-CELL INVASION complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Geobacter sulfurreducens (bacteria) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Gao, X. / Sun, D. / Cui, S. / Wang, Y. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structural Basis of prokaryotic Argonaute System Authors: Gao, X. / Cui, S. / Sun, D. / Wang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k87.cif.gz | 356.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k87.ent.gz | 272.9 KB | Display | PDB format |
PDBx/mmJSON format | 8k87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k87_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8k87_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8k87_validation.xml.gz | 53.5 KB | Display | |
Data in CIF | 8k87_validation.cif.gz | 79.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/8k87 ftp://data.pdbj.org/pub/pdb/validation_reports/k8/8k87 | HTTPS FTP |
-Related structure data
Related structure data | 36946MC 8k88C 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
#1: DNA chain | Mass: 12525.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: DNA/RNA hybrid | Mass: 6675.973 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Protein | Mass: 53325.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Gene: GSU1361 / Production host: Expression vector pET-mod (others) / References: UniProt: Q74DF5 #4: Protein | Mass: 66645.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Gene: GSU1360 / Production host: Expression vector pET-mod (others) / References: UniProt: Q74DF6 #5: Chemical | 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: dimmeric GsSirt2/ago-gRAN-tDNA complex / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: Geobacter sulfurreducens (bacteria) |
Source (recombinant) | Organism: Escherichia (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1 mg/ml / 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: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1103892 / Symmetry type: POINT | ||||||||||||||||||||||||
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