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- PDB-5zad: Human topoisomerase II beta in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 5zad
TitleHuman topoisomerase II beta in complex with DNA
Components
  • DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
  • DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')
  • DNA topoisomerase 2-beta
KeywordsDNA BINDING PROTEIN/DNA / DNA binding and cleavage / ISOMERASE-DNA complex / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / resolution of meiotic recombination intermediates / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / positive regulation of double-strand break repair via nonhomologous end joining / cellular response to ATP / DNA topological change / SUMOylation of DNA replication proteins / ribonucleoprotein complex binding ...positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / resolution of meiotic recombination intermediates / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / positive regulation of double-strand break repair via nonhomologous end joining / cellular response to ATP / DNA topological change / SUMOylation of DNA replication proteins / ribonucleoprotein complex binding / forebrain development / axonogenesis / B cell differentiation / neuron migration / cellular response to hydrogen peroxide / cellular senescence / ribonucleoprotein complex / chromatin binding / nucleolus / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol
Similarity search - Function
DTHCT / DTHCT (NUC029) region / DNA topoisomerase 2, TOPRIM domain / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / DNA topoisomerase II, eukaryotic-type / : / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A ...DTHCT / DTHCT (NUC029) region / DNA topoisomerase 2, TOPRIM domain / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / DNA topoisomerase II, eukaryotic-type / : / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA topoisomerase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsSun, L.Y. / Zhu, L.W. / Tang, Y.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21625602 China
CitationJournal: Sci Rep / Year: 2018
Title: Increasing the distance between two monomers of topoisomerase II beta under the action of antitumor agent 4 beta-sulfur-(benzimidazole) 4'-demethylepipodophyllotoxin.
Authors: Sun, L.Y. / Zhu, L.W. / Tang, Y.J.
History
DepositionFeb 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 2-beta
C: DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
F: DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')
B: DNA topoisomerase 2-beta
D: DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
E: DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)196,0396
Polymers196,0396
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11640 Å2
ΔGint-80 kcal/mol
Surface area70710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.006, 95.006, 230.289
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein DNA topoisomerase 2-beta / DNA topoisomerase II / beta isozyme


Mass: 91928.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOP2B / Production host: Escherichia coli (E. coli) / References: UniProt: Q02880, EC: 5.99.1.3
#2: DNA chain DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')


Mass: 2436.619 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')


Mass: 3654.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100mM magnesium chloride, 50mM sodium citrate, pH 5.3, 20% MPD, 0.05% ethyl acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97845 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97845 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 118178 / % possible obs: 99.5 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.045 / Rrim(I) all: 0.095 / Rsym value: 0.083 / Net I/σ(I): 15.711
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.9 % / Rmerge(I) obs: 3.017 / Mean I/σ(I) obs: 0.244 / Num. unique obs: 5596 / CC1/2: 0.12 / Rpim(I) all: 2.021 / Rrim(I) all: 3.653 / Rsym value: 3.017 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QX3

3qx3


Resolution: 2.54→28.064 Å / SU ML: 0.36 / Cross valid method: NONE / σ(F): 1.98 / Phase error: 25.28
RfactorNum. reflection% reflection
Rfree0.2274 3962 5.18 %
Rwork0.1802 --
obs0.1826 76508 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.54→28.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11784 820 0 90 12694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912952
X-RAY DIFFRACTIONf_angle_d1.25317627
X-RAY DIFFRACTIONf_dihedral_angle_d10.1410704
X-RAY DIFFRACTIONf_chiral_restr0.0891924
X-RAY DIFFRACTIONf_plane_restr0.0072127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.5710.31631080.31982674X-RAY DIFFRACTION100
2.571-2.60350.30171360.26682523X-RAY DIFFRACTION100
2.6035-2.63770.29731640.24242669X-RAY DIFFRACTION100
2.6377-2.67380.32561470.24322523X-RAY DIFFRACTION100
2.6738-2.7120.34942120.24992570X-RAY DIFFRACTION100
2.712-2.75250.302970.24192602X-RAY DIFFRACTION100
2.7525-2.79540.30561540.23862632X-RAY DIFFRACTION100
2.7954-2.84120.29921340.23372547X-RAY DIFFRACTION100
2.8412-2.89020.27551540.22812615X-RAY DIFFRACTION100
2.8902-2.94270.25751280.22162566X-RAY DIFFRACTION100
2.9427-2.99920.28841420.23362601X-RAY DIFFRACTION100
2.9992-3.06040.26641500.22592625X-RAY DIFFRACTION100
3.0604-3.12680.31741460.21282523X-RAY DIFFRACTION100
3.1268-3.19940.26441380.21852649X-RAY DIFFRACTION100
3.1994-3.27930.30521180.2182636X-RAY DIFFRACTION100
3.2793-3.36790.27391320.2082589X-RAY DIFFRACTION100
3.3679-3.46680.25781320.20442552X-RAY DIFFRACTION100
3.4668-3.57850.25081500.19122587X-RAY DIFFRACTION100
3.5785-3.70610.25911510.18562609X-RAY DIFFRACTION100
3.7061-3.85410.19891280.17212580X-RAY DIFFRACTION100
3.8541-4.02910.23031500.15962609X-RAY DIFFRACTION100
4.0291-4.24080.15481020.1582607X-RAY DIFFRACTION100
4.2408-4.50550.17011240.14122637X-RAY DIFFRACTION100
4.5055-4.85170.16681360.14022591X-RAY DIFFRACTION100
4.8517-5.3370.20911340.15382608X-RAY DIFFRACTION100
5.337-6.10230.24551800.18732537X-RAY DIFFRACTION100
6.1023-7.66230.19871980.17512522X-RAY DIFFRACTION99
7.6623-28.06570.16071170.13442563X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 21.957 Å / Origin y: -27.4652 Å / Origin z: -35.899 Å
111213212223313233
T0.5451 Å2-0.0053 Å2-0.0029 Å2-0.351 Å2-0.0362 Å2--0.4693 Å2
L0.2592 °2-0.0129 °20.0015 °2-0.7209 °2-0.3892 °2--0.9447 °2
S-0.1652 Å °0.0011 Å °0.0034 Å °0.0101 Å °0.0009 Å °-0.2549 Å °-0.0076 Å °0.0227 Å °0.1557 Å °
Refinement TLS groupSelection details: all

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