+Open data
-Basic information
Entry | Database: PDB / ID: 5gwk | ||||||
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Title | Human topoisomerase IIalpha in complex with DNA and etoposide | ||||||
Components |
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Keywords | ISOMERASE/DNA/ISOMERASE INHIBITOR / Type II topoisomerase / Anti-cancer drug / TopoII cleavage complex / ISOMERASE-DNA-ISOMERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information negative regulation of DNA duplex unwinding / positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / apoptotic chromosome condensation / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / resolution of meiotic recombination intermediates / female meiotic nuclear division / embryonic cleavage / DNA ligation / Transcription of E2F targets under negative control by DREAM complex ...negative regulation of DNA duplex unwinding / positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / apoptotic chromosome condensation / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / resolution of meiotic recombination intermediates / female meiotic nuclear division / embryonic cleavage / DNA ligation / Transcription of E2F targets under negative control by DREAM complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA binding, bending / DNA topological change / SUMOylation of DNA replication proteins / chromosome, centromeric region / ATP-dependent activity, acting on DNA / hematopoietic progenitor cell differentiation / condensed chromosome / protein kinase C binding / ubiquitin binding / male germ cell nucleus / chromosome segregation / regulation of circadian rhythm / rhythmic process / ribonucleoprotein complex / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / chromatin binding / nucleolus / magnesium ion binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.152 Å | ||||||
Authors | Wang, Y.R. / Wu, C.C. / Chan, N.L. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry Authors: Wang, Y.R. / Chen, S.F. / Wu, C.C. / Liao, Y.W. / Lin, T.S. / Liu, K.T. / Chen, Y.S. / Li, T.K. / Chien, T.C. / Chan, N.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gwk.cif.gz | 336.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gwk.ent.gz | 260.9 KB | Display | PDB format |
PDBx/mmJSON format | 5gwk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/5gwk ftp://data.pdbj.org/pub/pdb/validation_reports/gw/5gwk | HTTPS FTP |
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-Related structure data
Related structure data | 5gwiC 5gwjC 3qx3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 92917.750 Da / Num. of mol.: 2 / Fragment: UNP residues 430-1188 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TOP2A, TOP2 / Plasmid: pET51b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11388, EC: 5.99.1.3 #2: DNA chain | Mass: 2436.619 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 3654.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | ChemComp-MG / #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: Magnesium Acetate, 2-(N-morpholino)ethanesulfonic acid, 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→27.488 Å / Num. obs: 45909 / % possible obs: 99.2 % / Redundancy: 6.7 % / Rsym value: 0.48 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 3.15→3.2 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QX3 Resolution: 3.152→27.488 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.152→27.488 Å
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Refine LS restraints |
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LS refinement shell |
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