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- PDB-9bq7: Human Topoisomerase 2 Alpha ATPase domain bound to BNS22 and non-... -

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Basic information

Entry
Database: PDB / ID: 9bq7
TitleHuman Topoisomerase 2 Alpha ATPase domain bound to BNS22 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: 2.05 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)93,00711
Polymers90,9682
Non-polymers2,0399
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-52 kcal/mol
Surface area32070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.930, 92.847, 126.949
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, 302 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-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.: 2 / Source method: obtained synthetically / Formula: C24H25NO5 / 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.: 293 / 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: 2.27 Å3/Da / Density % sol: 45.7 %
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: Dec 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 52693 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.109 / Net I/σ(I): 19.4
Reflection shellResolution: 2.05→2.12 Å / Num. unique obs: 5172 / CC1/2: 0.496 / CC star: 0.814

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALEPACKdata scaling
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→47 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2632 1999 3.8 %
Rwork0.2247 --
obs0.2261 52588 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6144 0 132 293 6569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026402
X-RAY DIFFRACTIONf_angle_d0.5388650
X-RAY DIFFRACTIONf_dihedral_angle_d14.9172395
X-RAY DIFFRACTIONf_chiral_restr0.043955
X-RAY DIFFRACTIONf_plane_restr0.0031084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.090.39171230.38773116X-RAY DIFFRACTION87
2.09-2.150.39331430.35593625X-RAY DIFFRACTION100
2.15-2.210.30581420.32383571X-RAY DIFFRACTION100
2.21-2.290.39471410.30583597X-RAY DIFFRACTION100
2.29-2.370.32291420.30363612X-RAY DIFFRACTION100
2.37-2.460.39821430.2883606X-RAY DIFFRACTION100
2.46-2.570.29041440.27513625X-RAY DIFFRACTION100
2.57-2.710.3091430.26993627X-RAY DIFFRACTION100
2.71-2.880.30191430.25913633X-RAY DIFFRACTION100
2.88-3.10.3051450.24913634X-RAY DIFFRACTION100
3.1-3.410.21971450.22933669X-RAY DIFFRACTION100
3.41-3.910.30141450.20313687X-RAY DIFFRACTION100
3.91-4.920.21511460.17193711X-RAY DIFFRACTION100
4.92-470.18071540.16983876X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4621-1.5662-1.81834.65321.83776.0447-0.16040.1573-0.4313-0.29310.1880.09340.24940.11920.00580.4401-0.05990.08010.2395-0.00570.35618.3135-25.709926.1681
20.5157-0.30560.18223.33070.16690.9191-0.03310.1195-0.0101-0.97820.15471.9265-0.1687-0.2527-0.14020.547-0.0103-0.25940.3640.06590.7421-5.6403-12.868222.1522
33.82550.31760.85134.46070.08792.0751-0.1094-0.8416-0.1891.43660.11461.22160.0506-0.6930.06870.83620.10390.54560.65260.01161.08-7.3463-7.094647.4151
42.01350.1167-1.010.0238-0.05343.07950.0174-0.56950.58621.46830.3116-0.2812-0.30470.235-0.17150.97610.1131-0.04320.4295-0.17310.43168.9018-1.972846.6706
52.0590.9087-0.19541.06551.03481.94460.0641-0.32730.32451.06880.1753-0.38640.15450.2764-0.21960.6720.0463-0.04170.3628-0.11470.411912.4712-5.062141.7716
62.2780.13441.1840.00430.00185.42080.1266-0.83830.13051.67350.1151-0.29640.24310.0698-0.27861.6478-0.0177-0.05320.6909-0.20490.617610.88492.087455.832
77.7065-1.25263.76733.8044-0.5394.6165-0.48780.22440.6078-0.39760.1301-1.1265-0.41270.28250.33020.5984-0.10540.14760.2995-0.03580.599319.8928-6.529923.4954
80.7616-0.4343-0.02151.0777-0.17440.8905-0.4610.3613-0.2795-0.7492-0.1987-1.86320.00940.6976-0.97480.46890.02540.99880.5772-0.20051.695230.7321-21.760819.6988
91.9415-1.3427-0.14590.9622-0.05730.7861-0.19170.4635-0.0714-0.9259-0.0714-1.6979-0.01250.3847-0.17830.8465-0.1550.70580.7642-0.06771.835535.913-16.949216.7445
102.7752-0.0605-1.71422.5986-0.64981.2547-0.1961-0.89220.38380.5736-0.22-0.7229-0.31990.7540.42910.6007-0.0144-0.4140.95210.00842.120139.9349-21.900343.523
113.2305-0.16291.40921.8668-0.28694.2465-0.0779-0.7673-0.64051.36060.1771-1.33950.06570.2582-0.0910.80250.0588-0.38150.60980.06050.909724.2934-26.84746.1661
122.0804-0.1721-0.77842.16781.83381.7506-0.0371-1.0065-0.34541.04780.035-0.30670.1639-0.19760.00041.23330.0461-0.56310.9830.17380.818320.3212-23.38955.1266
133.4844-3.3420.79086.8954-1.33875.7235-0.1176-0.2857-0.36990.07660.2647-0.84980.2429-0.0514-0.11030.21180.02430.02560.3514-0.02870.5917.8041-26.499932.3018
141.9085-0.76050.17340.7754-0.35150.185-0.2063-1.21370.0321.83150.309-0.8492-0.10230.2097-0.1641.7180.055-0.69081.16540.1461.103423.6071-29.94457.014
150.0401-0.0405-0.17670.37480.23560.793-0.04160.0785-0.0958-0.09830.0463-0.23280.06710.42780.06540.5280.06760.59890.4422-0.01651.005426.9596-25.115319.0115
160.1384-0.03610.02240.0223-0.00850.0045-0.03240.0420.1024-0.11740.03770.2074-0.0711-0.1474-0.01270.52040.005-0.15790.3147-0.01250.36250.0046-7.880520.2906
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 249 )
3X-RAY DIFFRACTION3chain 'A' and (resid 250 through 288 )
4X-RAY DIFFRACTION4chain 'A' and (resid 289 through 343 )
5X-RAY DIFFRACTION5chain 'A' and (resid 344 through 387 )
6X-RAY DIFFRACTION6chain 'A' and (resid 388 through 417 )
7X-RAY DIFFRACTION7chain 'B' and (resid 28 through 68 )
8X-RAY DIFFRACTION8chain 'B' and (resid 69 through 183 )
9X-RAY DIFFRACTION9chain 'B' and (resid 184 through 249 )
10X-RAY DIFFRACTION10chain 'B' and (resid 250 through 288 )
11X-RAY DIFFRACTION11chain 'B' and (resid 289 through 341 )
12X-RAY DIFFRACTION12chain 'B' and (resid 342 through 366 )
13X-RAY DIFFRACTION13chain 'B' and (resid 367 through 387 )
14X-RAY DIFFRACTION14chain 'B' and (resid 388 through 417 )
15X-RAY DIFFRACTION15chain 'B' and (resid 901 through 901 )
16X-RAY DIFFRACTION16chain 'A' and (resid 901 through 901 )

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