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Yorodumi- PDB-8kgm: Structure of African swine fever virus topoisomerase II in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8kgm | ||||||
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Title | Structure of African swine fever virus topoisomerase II in complex with dsDNA | ||||||
Components |
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Keywords | VIRAL PROTEIN/DNA / topo 2 / VIRAL PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / host cell cytoplasm / DNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | African swine fever virus DNA molecule (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å | ||||||
Authors | Cong, J. / Xin, Y. / Li, X. / Chen, Y. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structure of African swine fever virus topoisomerase II in complex with dsDNA Authors: Jingyuan, C. / Yuhui, X. / Xuemei, L. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8kgm.cif.gz | 628.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8kgm.ent.gz | 509.1 KB | Display | PDB format |
PDBx/mmJSON format | 8kgm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/8kgm ftp://data.pdbj.org/pub/pdb/validation_reports/kg/8kgm | HTTPS FTP |
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-Related structure data
Related structure data | 37226MC 8kglC 8kgnC 8kgoC 8kgpC 8kgqC 8kgrC 8kgsC 8kgtC 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: 138093.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) African swine fever virus / Gene: P1192R CDS / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2X0THW2 #2: DNA chain | | Mass: 16058.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others) #3: DNA chain | | Mass: 15965.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others) |
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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: pP1192R / Type: COMPLEX / Details: dimer / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: African swine fever virus |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.2 |
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 FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19000 / Symmetry type: POINT | ||||||||||||||||||||||||
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