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Yorodumi- PDB-8kgs: Structure of African swine fever virus topoisomerase II in comple... -
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-Basic information
Entry | Database: PDB / ID: 8kgs | ||||||
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Title | Structure of African swine fever virus topoisomerase II in complex with dsDNA | ||||||
Components | DNA topoisomerase 2 | ||||||
Keywords | VIRAL PROTEIN / topo 2 | ||||||
Function / homology | Function and homology information sister chromatid segregation / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | African swine fever virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.603 Å | ||||||
Authors | Cong, J. / Xin, Y. / Li, X. / Chen, Y. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural insights into the DNA topoisomerase II of the African swine fever virus. Authors: Jingyuan Cong / Yuhui Xin / Huiling Kang / Yunge Yang / Chenlong Wang / Dongming Zhao / Xuemei Li / Zihe Rao / Yutao Chen / Abstract: Type II topoisomerases are ubiquitous enzymes that play a pivotal role in modulating the topological configuration of double-stranded DNA. These topoisomerases are required for DNA metabolism and ...Type II topoisomerases are ubiquitous enzymes that play a pivotal role in modulating the topological configuration of double-stranded DNA. These topoisomerases are required for DNA metabolism and have been extensively studied in both prokaryotic and eukaryotic organisms. However, our understanding of virus-encoded type II topoisomerases remains limited. One intriguing example is the African swine fever virus, which stands as the sole mammalian-infecting virus encoding a type II topoisomerase. In this work, we use several approaches including cryo-EM, X-ray crystallography, and biochemical assays to investigate the structure and function of the African swine fever virus type II topoisomerase, pP1192R. We determine the structures of pP1192R in different conformational states and confirm its enzymatic activity in vitro. Collectively, our results illustrate the basic mechanisms of viral type II topoisomerases, increasing our understanding of these enzymes and presenting a potential avenue for intervention strategies to mitigate the impact of the African swine fever virus. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8kgs.cif.gz | 174.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8kgs.ent.gz | 137.3 KB | Display | PDB format |
PDBx/mmJSON format | 8kgs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8kgs_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8kgs_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8kgs_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 8kgs_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/8kgs ftp://data.pdbj.org/pub/pdb/validation_reports/kg/8kgs | HTTPS FTP |
-Related structure data
Related structure data | 8kglC 8kgmC 8kgnC 8kgoC 8kgpC 8kgqC 8kgrC 8kgtC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 49519.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) African swine fever virus / Gene: P1192R CDS / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2X0THW2 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ANP / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.52 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 21% PEG 3350, 100 mM Hepes (pH 7.2) and 200 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 14604 / % possible obs: 100 % / Redundancy: 19 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.203 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 9 % / Rmerge(I) obs: 1.019 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 708 / CC1/2: 0.76 / CC star: 0.929 / Rpim(I) all: 0.339 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.603→42.78 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.603→42.78 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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