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- PDB-9bqd: Human Topoisomerase 2 Beta ATPase domain bound to topobexin and n... -

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Basic information

Entry
Database: PDB / ID: 9bqd
TitleHuman Topoisomerase 2 Beta ATPase domain bound to topobexin and non-hydrolyzable ATP analog AMPPNP
ComponentsDNA topoisomerase 2-beta
KeywordsISOMERASE/INHIBITOR / Topoisomerase / ATPase / HYDROLASE / ISOMERASE-INHIBITOR 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 / positive regulation of double-strand break repair via nonhomologous end joining / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / cellular response to ATP / forebrain development / DNA topological change / SUMOylation of DNA replication proteins ...positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / resolution of meiotic recombination intermediates / positive regulation of double-strand break repair via nonhomologous end joining / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / cellular response to ATP / forebrain development / DNA topological change / SUMOylation of DNA replication proteins / ribonucleoprotein complex binding / axonogenesis / B cell differentiation / cellular response to hydrogen peroxide / neuron migration / cellular senescence / ribonucleoprotein complex / chromatin binding / nucleolus / DNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / 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 superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
: / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA topoisomerase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCong, A.T.Q. / Austin, C.A. / Kubes, J. / Karabanovich, G. / Melnikova, I. / Lencova, O. / Kollarova, P. / Piskackova, H.B. / Kerestes, V. / Applova, L. ...Cong, A.T.Q. / Austin, C.A. / Kubes, J. / Karabanovich, G. / Melnikova, I. / Lencova, O. / Kollarova, P. / Piskackova, H.B. / Kerestes, V. / Applova, L. / Arrouye, L. / Alvey, J.A. / Paluncic, J. / Witter, T.L. / Jirkovska, A. / Kunes, J. / Sterbova, P. / Sterba, M. / Simunek, T. / Roh, J. / Schellenberg, M.J.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Commun / Year: 2025
Title: Topobexin targets the Topoisomerase II ATPase domain for beta isoform-selective inhibition and anthracycline cardioprotection.
Authors: Kubes, J. / Karabanovich, G. / Cong, A.T.Q. / Melnikova, I. / Lencova, O. / Kollarova, P. / Bavlovic Piskackova, H. / Kerestes, V. / Applova, L. / Arrouye, L.C.M. / Alvey, J.R. / Paluncic, J. ...Authors: Kubes, J. / Karabanovich, G. / Cong, A.T.Q. / Melnikova, I. / Lencova, O. / Kollarova, P. / Bavlovic Piskackova, H. / Kerestes, V. / Applova, L. / Arrouye, L.C.M. / Alvey, J.R. / Paluncic, J. / Witter, T.L. / Jirkovska, A. / Kunes, J. / Sterbova-Kovarikova, P. / Austin, C.A. / Sterba, M. / Simunek, T. / Roh, J. / Schellenberg, M.J.
History
DepositionMay 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2824
Polymers45,2621
Non-polymers1,0203
Water6,900383
1
A: DNA topoisomerase 2-beta
hetero molecules

A: DNA topoisomerase 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5648
Polymers90,5242
Non-polymers2,0406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8980 Å2
ΔGint-41 kcal/mol
Surface area31890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.940, 83.940, 127.124
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 45262.066 Da / Num. of mol.: 1 / Fragment: residues 50-443 (Uniprot numbering)
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, DNA topoisomerase (ATP-hydrolysing)
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-A1ASC / 8-(3,4-dihydroquinoline-1(2H)-carbonyl)-7-[2-(4-methylpiperazin-1-yl)ethoxy]-4-propyl-2H-1-benzopyran-2-one / topobexin


Mass: 489.606 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H35N3O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 18% PEG3350, 0.2M potassium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 73237 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.022 / Rrim(I) all: 0.082 / Χ2: 1.027 / Net I/σ(I): 8 / Num. measured all: 961190
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.5-1.5513.12.21872140.4270.7730.6252.3061.015100
1.55-1.6213.31.56671800.620.8750.441.6271.002100
1.62-1.6913.21.0372320.7990.9420.2921.0721.021100
1.69-1.7812.50.62272100.9080.9760.1820.6491.04100
1.78-1.8913.20.34872610.9730.9930.0990.3621.07999.8
1.89-2.0413.70.19972690.9910.9980.0550.2071.079100
2.04-2.2413.40.11673280.9970.9990.0330.120.993100
2.24-2.5612.30.07573420.9980.9990.0220.0781.023100
2.56-3.2313.90.04974340.99910.0140.0511.043100
3.23-5012.60.03677670.99910.010.0380.97599.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALEPACKdata scaling
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→43.38 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1616 2000 2.76 %
Rwork0.1314 --
obs0.1322 72408 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→43.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 68 383 3558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083313
X-RAY DIFFRACTIONf_angle_d1.1264486
X-RAY DIFFRACTIONf_dihedral_angle_d14.1671265
X-RAY DIFFRACTIONf_chiral_restr0.084493
X-RAY DIFFRACTIONf_plane_restr0.011559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.33941360.25544795X-RAY DIFFRACTION96
1.54-1.580.28151380.21484850X-RAY DIFFRACTION97
1.58-1.630.23031400.18864908X-RAY DIFFRACTION98
1.63-1.680.23851390.17954945X-RAY DIFFRACTION98
1.68-1.740.18681410.15264943X-RAY DIFFRACTION99
1.74-1.810.19131410.12714955X-RAY DIFFRACTION99
1.81-1.890.15941420.10854998X-RAY DIFFRACTION99
1.89-1.990.16161430.11255040X-RAY DIFFRACTION100
1.99-2.110.15741430.11635032X-RAY DIFFRACTION100
2.11-2.280.14421440.10595086X-RAY DIFFRACTION100
2.28-2.510.15481450.11335084X-RAY DIFFRACTION100
2.51-2.870.16461460.12485131X-RAY DIFFRACTION100
2.87-3.610.16161480.1265202X-RAY DIFFRACTION100
3.62-43.380.13521540.14015439X-RAY DIFFRACTION100

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