+Open data
-Basic information
Entry | Database: PDB / ID: 9ca1 | |||||||||
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Title | Human TOP3B-TDRD3 core complex in DNA religation state | |||||||||
Components |
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Keywords | ISOMERASE/DNA / Topoisomerase / DNA / ISOMERASE-DNA complex | |||||||||
Function / homology | Function and homology information DNA topoisomerase III-beta-TDRD3 complex / DNA topoisomerase activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / condensed chromosome / methylated histone binding / chromosome segregation / chromatin organization / DNA recombination ...DNA topoisomerase III-beta-TDRD3 complex / DNA topoisomerase activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / condensed chromosome / methylated histone binding / chromosome segregation / chromatin organization / DNA recombination / transcription coactivator activity / DNA repair / chromatin binding / Golgi apparatus / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å | |||||||||
Authors | Yang, X. / Chen, X. / Yang, W. / Pommier, Y. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Structural Insights into human Topoisomerase 3-beta DNA and RNA catalytic cycles and topo-gate dynamics Authors: Yang, X. / Chen, X. / Yang, W. / Pommier, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9ca1.cif.gz | 150.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9ca1.ent.gz | 113.4 KB | Display | PDB format |
PDBx/mmJSON format | 9ca1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9ca1_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 9ca1_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 9ca1_validation.xml.gz | 35.2 KB | Display | |
Data in CIF | 9ca1_validation.cif.gz | 49.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/9ca1 ftp://data.pdbj.org/pub/pdb/validation_reports/ca/9ca1 | HTTPS FTP |
-Related structure data
Related structure data | 45379MC 9c9yC 9ca0C 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: 69119.867 Da / Num. of mol.: 1 / Mutation: K10M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TOP3B, TOP3B1 / Production host: Homo sapiens (human) / References: UniProt: O95985, DNA topoisomerase | ||
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#2: Protein | Mass: 17428.951 Da / Num. of mol.: 1 / Fragment: DUF-OB fold (UNP residues 1-161) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TDRD3 / Production host: Homo sapiens (human) / References: UniProt: Q9H7E2 | ||
#3: DNA chain | Mass: 2105.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||
#4: DNA chain | Mass: 876.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||
#5: Chemical | Has ligand of interest | Y | |
-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: human TOP3B-TDRD3 core complex with DNA / Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 6.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 46 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: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 901517 / Symmetry type: POINT |