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- PDB-9bqb: Human Topoisomerase 2 Alpha ATPase domain bound to topobexin and ... -

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Basic information

Entry
Database: PDB / ID: 9bqb
TitleHuman Topoisomerase 2 Alpha ATPase domain bound to topobexin and non-hydrolyzable ATP analog AMPPNP
ComponentsDNA topoisomerase 2-alpha
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 / apoptotic chromosome condensation / sister chromatid segregation / resolution of meiotic recombination intermediates / female meiotic nuclear division / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / embryonic cleavage / Transcription of E2F targets under negative control by DREAM complex / DNA binding, bending ...positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / apoptotic chromosome condensation / sister chromatid segregation / resolution of meiotic recombination intermediates / female meiotic nuclear division / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / embryonic cleavage / Transcription of E2F targets under negative control by DREAM complex / DNA binding, bending / DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / SUMOylation of DNA replication proteins / chromosome, centromeric region / ATP-dependent activity, acting on DNA / hematopoietic progenitor cell differentiation / condensed chromosome / male germ cell nucleus / ubiquitin binding / protein kinase C binding / chromosome segregation / regulation of circadian rhythm / rhythmic process / chromatin organization / positive regulation of apoptotic process / protein heterodimerization activity / ribonucleoprotein complex / 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
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
: / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA topoisomerase 2-alpha
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-alpha
B: DNA topoisomerase 2-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,17211
Polymers90,9682
Non-polymers2,2039
Water11,512639
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-60 kcal/mol
Surface area31720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.798, 92.536, 125.585
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 45484.211 Da / Num. of mol.: 2 / Fragment: residues 29-424
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOP2A, TOP2 / Production host: Escherichia coli (E. coli)
References: UniProt: P11388, DNA topoisomerase (ATP-hydrolysing)

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Non-polymers , 6 types, 648 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: 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.: 2 / Source method: obtained synthetically / Formula: C29H35N3O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 639 / 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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG3350 (w/v), 0.2M NH4Cl, 0.1M Tris pH 8.0

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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: 1.5→50 Å / Num. obs: 130369 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.02 / Rrim(I) all: 0.075 / Χ2: 1.003 / Net I/σ(I): 9.3 / Num. measured all: 1718606
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.5-1.5512.91.536129030.6060.8690.4411.60.989100
1.55-1.6213.41.163128730.7770.9350.3271.2080.975100
1.62-1.6913.10.775129410.8890.970.2210.8060.984100
1.69-1.78120.494128920.9410.9850.1470.5161.0199.6
1.78-1.8913.90.315129540.9810.9950.0870.3271.016100
1.89-2.0413.80.18129730.9930.9980.050.1871.019100
2.04-2.2413.40.113130050.9970.9990.0320.1170.978100
2.24-2.5612.40.078130750.9980.9990.0230.0821.005100
2.56-3.23140.055131660.99910.0150.0571.033100
3.23-5012.80.039135870.99910.0110.0411.01399.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALEPACKdata scaling
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→46.68 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1759 2000 1.54 %
Rwork0.1397 --
obs0.1403 130275 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6176 0 144 639 6959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076560
X-RAY DIFFRACTIONf_angle_d1.0118881
X-RAY DIFFRACTIONf_dihedral_angle_d17.2742486
X-RAY DIFFRACTIONf_chiral_restr0.058981
X-RAY DIFFRACTIONf_plane_restr0.0061107
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.29971390.23518975X-RAY DIFFRACTION99
1.54-1.580.25431420.20429082X-RAY DIFFRACTION100
1.58-1.630.23731420.18629100X-RAY DIFFRACTION100
1.63-1.680.20721420.16069060X-RAY DIFFRACTION100
1.68-1.740.16971410.14699071X-RAY DIFFRACTION100
1.74-1.810.23021420.13829088X-RAY DIFFRACTION100
1.81-1.890.19081420.13099125X-RAY DIFFRACTION100
1.89-1.990.16931420.12439120X-RAY DIFFRACTION100
1.99-2.110.15951430.11639169X-RAY DIFFRACTION100
2.11-2.280.16581420.1179138X-RAY DIFFRACTION100
2.28-2.510.14951440.12269193X-RAY DIFFRACTION100
2.51-2.870.16661440.13059224X-RAY DIFFRACTION100
2.87-3.620.16421460.13959321X-RAY DIFFRACTION100
3.62-46.680.17651490.14899609X-RAY DIFFRACTION100

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