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- PDB-9bqa: Human Topoisomerase 2 Beta ATPase domain bound to BNS22 and non-h... -

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Basic information

Entry
Database: PDB / ID: 9bqa
TitleHuman Topoisomerase 2 Beta ATPase domain bound to BNS22 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 / 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 / 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 / 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 / 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: 1.9 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)46,2925
Polymers45,2621
Non-polymers1,0304
Water3,873215
1
A: DNA topoisomerase 2-beta
hetero molecules

A: DNA topoisomerase 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,58410
Polymers90,5242
Non-polymers2,0608
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9320 Å2
ΔGint-29 kcal/mol
Surface area31560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.004, 84.004, 126.686
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#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)

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Non-polymers , 5 types, 219 molecules

#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-A1ASD / 8-(3,4-dihydroquinoline-1(2H)-carbonyl)-5,7-dimethoxy-4-propyl-2H-1-benzopyran-2-one / BNS22


Mass: 407.459 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25NO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 50.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 20% PEG3350, 0.2M potassium citrate, 0.1M tris pH 9.0

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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: 1.9→50 Å / Num. obs: 36618 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.034 / Rrim(I) all: 0.123 / Χ2: 1.048 / Net I/σ(I): 7.2 / Num. measured all: 465333
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) all% possible allRrim(I) allΧ2
1.9-1.9712.41.77735830.6020.8670.524100
1.97-2.0513.11.25436120.7790.9360.3591001.3060.934
2.05-2.1412.20.83235880.8670.9640.2461000.8690.96
2.14-2.2512.10.55935900.930.9820.16799.90.5841.029
2.25-2.3913.20.38636250.9710.9930.1199.90.4011.03
2.39-2.5813.50.24336270.9880.9970.0681000.2531.091
2.58-2.8413.10.15336530.9940.9990.0441000.1591.067
2.84-3.2512.20.08836840.9970.9990.02699.90.0921.087
3.25-4.0913.10.06137150.99810.01899.70.0631.089
4.09-5012.30.04839410.9950.9990.01499.90.051.077

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALEPACKdata scaling
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→43.33 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1943 1999 5.52 %
Rwork0.1671 --
obs0.1686 36224 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→43.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 68 215 3390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053269
X-RAY DIFFRACTIONf_angle_d0.8384420
X-RAY DIFFRACTIONf_dihedral_angle_d13.0481227
X-RAY DIFFRACTIONf_chiral_restr0.05488
X-RAY DIFFRACTIONf_plane_restr0.007549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.3551350.39552314X-RAY DIFFRACTION95
1.94-20.24331380.24432380X-RAY DIFFRACTION98
2-2.060.27851400.20942385X-RAY DIFFRACTION99
2.06-2.120.23151410.1952416X-RAY DIFFRACTION99
2.12-2.20.20891410.18092405X-RAY DIFFRACTION99
2.2-2.290.25721400.20972398X-RAY DIFFRACTION99
2.29-2.390.21711420.16232427X-RAY DIFFRACTION99
2.39-2.520.17691410.15522422X-RAY DIFFRACTION99
2.52-2.670.18491420.16182447X-RAY DIFFRACTION100
2.67-2.880.21021450.17522458X-RAY DIFFRACTION99
2.88-3.170.18771440.16272470X-RAY DIFFRACTION100
3.17-3.630.19251460.15652498X-RAY DIFFRACTION100
3.63-4.570.13721480.13152528X-RAY DIFFRACTION100
4.57-43.330.19331560.1582677X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 4.2043 Å / Origin y: 24.4911 Å / Origin z: 2.8901 Å
111213212223313233
T0.1668 Å20.0112 Å2-0.0362 Å2-0.1985 Å2-0.0069 Å2--0.1709 Å2
L0.9195 °20.0024 °2-0.1987 °2-1.4824 °2-0.2136 °2--1.2184 °2
S0.019 Å °-0.0001 Å °0.024 Å °-0.0369 Å °0.033 Å °0.0358 Å °-0.0649 Å °-0.0932 Å °-0.0422 Å °
Refinement TLS groupSelection details: all

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