+Open data
-Basic information
Entry | Database: PDB / ID: 8jsi | ||||||
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Title | Cryo-EM structure of a DNA-protein complex | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / DNA / protein / interaction / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermococcus thioreducens (archaea) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Li, Z. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Cryo-EM structure of a DNA-protein complex 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 | 8jsi.cif.gz | 337.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jsi.ent.gz | 267.9 KB | Display | PDB format |
PDBx/mmJSON format | 8jsi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jsi_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8jsi_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8jsi_validation.xml.gz | 53.9 KB | Display | |
Data in CIF | 8jsi_validation.cif.gz | 79.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/8jsi ftp://data.pdbj.org/pub/pdb/validation_reports/js/8jsi | HTTPS FTP |
-Related structure data
Related structure data | 36621MC 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: Protein | Mass: 87488.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus thioreducens (archaea) / Gene: A3L14_06700 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0Q2M2Z1 #2: DNA chain | Mass: 4747.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermococcus thioreducens (archaea) #3: DNA chain | Mass: 5049.273 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermococcus thioreducens (archaea) #4: Chemical | ChemComp-ZN / | #5: Chemical | ChemComp-MG / 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: a DNA-protein complex / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Thermococcus thioreducens (archaea) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
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
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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 629194 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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