PDB-9bq6: Human Topoisomerase 2 Alpha ATPase domain bound to non-hydrolyzab...

ID or keywords:

Entry

Database: PDB / ID: 9bq6

Title

Human Topoisomerase 2 Alpha ATPase domain bound to non-hydrolyzable ATP analog AMPPNP

Components

DNA topoisomerase 2-alpha

Keywords

ISOMERASE / Topoisomerase / ATPase / HYDROLASE

Function / homology

Function and homology information

apoptotic chromosome condensation / positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / resolution of meiotic recombination intermediates / female meiotic nuclear division / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / embryonic cleavage / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / Transcription of E2F targets under negative control by DREAM complex / DNA binding, bending ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Paluncic, J. / Witter, T.L. / Kubes, J. / Karabanovich, G. / Cong, A.T.Q. / Melnikova, I. / Lencova, O. / Kollarova, P. / Piskackova, H.B. / Kerestes, V. ...

Funding support

1items

Citation

Journal: 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. ...

History

Deposition	May 9, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 25, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9bq6.cif.gz	475.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9bq6.ent.gz	396.3 KB	Display	PDB format
PDBx/mmJSON format	9bq6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9bq6_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	9bq6_full_validation.pdf.gz	1 MB	Display
Data in XML	9bq6_validation.xml.gz	38.6 KB	Display
Data in CIF	9bq6_validation.cif.gz	52 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bq/9bq6 ftp://data.pdbj.org/pub/pdb/validation_reports/bq/9bq6	HTTPS FTP

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Related structure data

Related structure data	9bq7C 9bq8C 9bq9C 9bqaC 9bqbC 9bqcC 9bqdC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#73 - Jan 2006 Topoisomerase similarity (23) #131 - Nov 2010 Inteins similarity (6) #150 - Jun 2012 Sliding Clamps similarity (2) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #168 - Dec 2013 DNA Helicase similarity (3) #160 - Apr 2013 Actinomycin similarity (1) #108 - Dec 2008 Hsp90 similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#73 - Jan 2006
Topoisomerase
similarity (23)
#131 - Nov 2010
Inteins
similarity (6)
#150 - Jun 2012
Sliding Clamps
similarity (2)
#205 - Jan 2017
Nuclear Pore Complex
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (3)
#160 - Apr 2013
Actinomycin
similarity (1)
#108 - Dec 2008
Hsp90
similarity (1)
#182 - Feb 2015
Insulin receptor
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#50 - Feb 2004
Glycolytic Enzymes
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#80 - Aug 2006
AAA+ Proteases
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: DNA topoisomerase 2-alpha

B: DNA topoisomerase 2-alpha

hetero molecules

92 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	69.781, 92.699, 125.464
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#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)
#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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.85 %
Crystal grow	Temperature: 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

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-E / Wavelength: 0.97918 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2021

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 1.9→50 Å / Num. obs: 64775 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC_1/2: 0.998 / CC star: 0.999 / R_merge(I) obs: 0.095 / R_pim(I) all: 0.039 / R_rim(I) all: 0.103 / Χ²: 1.019 / Net I/σ(I): 7.5 / Num. measured all: 442076

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.9-1.97	6.8	1.403	6370	0.527	0.831	0.577	1.519	0.984	99.6
1.97-2.05	7.1	0.899	6381	0.779	0.936	0.362	0.97	0.992	100
2.05-2.14	6.9	0.669	6406	0.853	0.96	0.273	0.724	1.039	99.9
2.14-2.25	6.6	0.453	6430	0.925	0.98	0.19	0.492	1.064	99.9
2.25-2.39	6.6	0.323	6402	0.954	0.988	0.135	0.35	1.063	99.8
2.39-2.58	7.2	0.222	6460	0.978	0.995	0.088	0.239	1.041	99.9
2.58-2.84	7.1	0.149	6451	0.989	0.997	0.06	0.161	1.011	99.9
2.84-3.25	6.6	0.097	6498	0.994	0.998	0.041	0.105	0.997	100
3.25-4.09	6.8	0.068	6555	0.996	0.999	0.028	0.074	1.01	99.7
4.09-50	6.5	0.056	6822	0.997	0.999	0.024	0.061	0.993	99.8

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
SCALEPACK		data scaling
DENZO		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→46.65 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1958	2089	3.23 %
R_work	0.1764	-	-
obs	0.177	64689	99.41 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.9→46.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6258	0	0	398	6656

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6396
X-RAY DIFFRACTION	f_angle_d	1.033	8641
X-RAY DIFFRACTION	f_dihedral_angle_d	14.241	2404
X-RAY DIFFRACTION	f_chiral_restr	0.059	961
X-RAY DIFFRACTION	f_plane_restr	0.006	1086

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9-1.94	0.3023	128	0.2911	3855	X-RAY DIFFRACTION	93
1.94-1.99	0.2708	136	0.2635	4121	X-RAY DIFFRACTION	100
1.99-2.04	0.241	138	0.2343	4147	X-RAY DIFFRACTION	100
2.04-2.1	0.2695	140	0.2219	4152	X-RAY DIFFRACTION	100
2.1-2.17	0.2546	137	0.2144	4137	X-RAY DIFFRACTION	100
2.17-2.25	0.2469	142	0.2005	4173	X-RAY DIFFRACTION	100
2.25-2.34	0.2221	136	0.1889	4123	X-RAY DIFFRACTION	100
2.34-2.45	0.2334	141	0.1814	4164	X-RAY DIFFRACTION	100
2.45-2.58	0.2023	138	0.1811	4202	X-RAY DIFFRACTION	100
2.58-2.74	0.1926	141	0.1772	4146	X-RAY DIFFRACTION	100
2.74-2.95	0.2032	141	0.1859	4208	X-RAY DIFFRACTION	100
2.95-3.24	0.2189	139	0.1817	4215	X-RAY DIFFRACTION	100
3.24-3.71	0.1739	142	0.1615	4234	X-RAY DIFFRACTION	100
3.71-4.68	0.1574	142	0.1433	4275	X-RAY DIFFRACTION	100
4.68-46.65	0.1779	148	0.1715	4448	X-RAY DIFFRACTION	100

Refinement TLS params.

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

ID	L11 (°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)
1	2.6359	-0.0351	-1.5706	3.6154	0.7562	3.8505	-0.2169	0.1897	-0.3648	-0.2243	0.1448	0.0416	0.4555	-0.1812	0.0837	0.2472	-0.0201	0.0167	0.219	0.0167	0.251	7.9177	-25.6603	26.1641
2	1.9089	0.0568	0.3383	3.6372	0.5425	1.6683	-0.059	0.2108	0.0233	-0.6517	0.002	0.8616	-0.202	-0.2906	-0.0394	0.3087	0.0223	-0.1155	0.2874	0.0016	0.3537	-5.5881	-12.714	21.8287
3	2.37	0.2643	1.3581	1.7927	0.025	3.3967	0.0157	-0.9046	0.082	0.9571	0.0592	0.899	-0.3482	-0.6007	-0.1601	0.6338	0.0464	0.3229	0.5362	0.0074	0.6067	-7.338	-6.8028	47.0551
4	2.576	-0.475	0.1049	0.9618	-0.0243	2.0725	0.1184	-0.4987	0.4317	1.1293	-0.0329	0.1008	-0.2259	0.1862	-0.062	0.621	-0.0412	0.0619	0.3581	-0.0629	0.2383	8.8312	-1.9752	46.4977
5	1.2966	0.3527	-0.2809	1.758	1.0365	1.5897	0.1733	-0.4035	0.0543	0.6858	0.0086	-0.159	0.1289	0.2695	-0.1393	0.4122	-0.0238	-0.0063	0.3706	-0.0257	0.2458	12.7304	-5.2429	41.5936
6	1.2601	-0.1083	-0.4718	0.1067	0.3194	0.9196	0.0063	-0.8665	0.1367	1.3139	-0.1725	-0.1557	-0.5487	0.2075	-0.0686	1.1738	-0.0987	0.0264	0.6809	-0.0928	0.414	11.9338	0.2229	57.0591
7	3.3196	-0.5055	1.1725	3.3047	0.2111	1.7234	-0.1161	0.075	0.1727	-0.2469	0.1994	-0.5798	-0.341	0.1593	-0.0474	0.4519	-0.0586	0.1055	0.3078	-0.036	0.329	20.0891	-6.7413	23.4862
8	2.663	-0.3699	0.0295	2.4104	-0.7234	1.721	-0.2085	0.3399	-0.2889	-0.9126	0.317	-1.7018	-0.1573	0.4956	-0.1625	0.4569	-0.0895	0.4331	0.5371	-0.1931	0.9071	32.4274	-20.3113	18.2851
9	2.0289	0.5064	-1.7045	5.4765	-0.8095	1.4958	0.2452	-1.0046	-0.1596	1.2088	0.1191	-1.4973	-0.1712	0.8657	0.4555	0.3356	0.0427	-0.4247	1.0053	-0.1726	1.4273	39.6659	-22.4678	43.2333
10	1.9027	0.3779	0.4069	2.3588	-0.4069	2.6981	0.0802	-0.6894	-0.3042	0.8881	0.0796	-0.5378	0.0494	0.0093	-0.1749	0.526	0.0418	-0.1603	0.6036	0.0462	0.4664	21.5851	-26.3138	44.9793
11	1.5336	-0.1878	0.2285	0.7305	-0.7999	0.8639	-0.1717	-1.1521	0.1003	1.6024	0.0704	-0.5977	0.2188	-0.2126	0.1534	1.2323	0.0793	-0.4507	1.1114	0.1172	0.7841	23.1379	-30.1621	56.3161

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 28 through 68 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 69 through 249 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 250 through 288 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 289 through 343 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 344 through 387 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 388 through 418 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 28 through 69 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 70 through 249 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 250 through 288 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 289 through 387 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 388 through 415 )

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