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- PDB-9bqc: Human Topoisomerase 2 Beta ATPase domain bound to obex 5c and non... -

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Basic information

Entry
Database: PDB / ID: 9bqc
TitleHuman Topoisomerase 2 Beta ATPase domain bound to obex 5c 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 negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / cellular response to ATP / positive regulation of double-strand break repair via nonhomologous end joining / 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 negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / cellular response to ATP / positive regulation of double-strand break repair via nonhomologous end joining / DNA topological change / SUMOylation of DNA replication proteins / ribonucleoprotein complex binding / forebrain development / B cell differentiation / axonogenesis / 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 / 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: 1.45 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)46,2004
Polymers45,2621
Non-polymers9383
Water7,170398
1
A: DNA topoisomerase 2-beta
hetero molecules

A: DNA topoisomerase 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4008
Polymers90,5242
Non-polymers1,8766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8730 Å2
ΔGint-47 kcal/mol
Surface area31880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.148, 84.148, 127.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1169-

HOH

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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-A1ASE / 8-(3,4-dihydroquinoline-1(2H)-carbonyl)-7-(2-hydroxyethoxy)-4-propyl-2H-1-benzopyran-2-one / obex 5c


Mass: 407.459 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25NO5 / 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.: 398 / 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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 17% PEG3350, 0.1M potassium citrate, 0.1M HEPES pH7.0

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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: Dec 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 81673 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.018 / Rrim(I) all: 0.05 / Χ2: 0.998 / Net I/σ(I): 10.5 / Num. measured all: 603596
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.45-1.57.51.22880410.5690.8520.471.3170.94599.9
1.5-1.567.50.8280330.7560.9280.3130.8780.94899.9
1.56-1.637.40.53180400.8850.9690.2050.570.95699.9
1.63-1.726.90.33480720.9420.9850.1350.3610.97899.8
1.72-1.837.50.280960.9830.9960.0770.2151.008100
1.83-1.977.70.11881080.9940.9980.0450.1261.046100
1.97-2.177.50.0781730.9970.9990.0270.0751.053100
2.17-2.486.90.04881880.99810.020.0521.01799.9
2.48-3.127.80.03882820.99910.0140.0410.992100
3.12-507.10.03186400.99910.0130.0341.03299.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALEPACKdata scaling
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→43.54 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1717 2000 2.47 %
Rwork0.1559 --
obs0.1562 81098 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 62 398 3567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073285
X-RAY DIFFRACTIONf_angle_d1.0134448
X-RAY DIFFRACTIONf_dihedral_angle_d13.9641234
X-RAY DIFFRACTIONf_chiral_restr0.08491
X-RAY DIFFRACTIONf_plane_restr0.009556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.28091380.27825448X-RAY DIFFRACTION97
1.49-1.530.2771390.2375514X-RAY DIFFRACTION98
1.53-1.570.19171400.21385508X-RAY DIFFRACTION99
1.57-1.620.20421400.20415579X-RAY DIFFRACTION99
1.62-1.680.241410.20145563X-RAY DIFFRACTION99
1.68-1.750.20091410.18885583X-RAY DIFFRACTION99
1.75-1.830.191420.16795624X-RAY DIFFRACTION100
1.83-1.920.19621430.15345624X-RAY DIFFRACTION100
1.92-2.040.18461430.15825658X-RAY DIFFRACTION100
2.04-2.20.17891430.14955689X-RAY DIFFRACTION100
2.2-2.420.15791450.14335697X-RAY DIFFRACTION100
2.42-2.770.17571440.14765737X-RAY DIFFRACTION100
2.77-3.490.15771470.14865817X-RAY DIFFRACTION100
3.49-43.540.1521540.14516057X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 3.9166 Å / Origin y: 24.6203 Å / Origin z: 3.1133 Å
111213212223313233
T0.1193 Å20.0063 Å2-0.0315 Å2-0.1473 Å2-0.015 Å2--0.1337 Å2
L0.8258 °20.043 °2-0.3148 °2-1.1004 °2-0.1928 °2--0.931 °2
S0.0105 Å °0.0161 Å °-0.0032 Å °-0.0242 Å °0.0231 Å °0.0306 Å °-0.046 Å °-0.0695 Å °-0.0247 Å °
Refinement TLS groupSelection details: all

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