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- PDB-7qfn: Human Topoisomerase II Beta ATPase ADP -

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Basic information

Entry
Database: PDB / ID: 7qfn
TitleHuman Topoisomerase II Beta ATPase ADP
ComponentsDNA topoisomerase 2-beta
KeywordsDNA BINDING PROTEIN / DNA Topoisomerase II Beta / Human / ATPase Domain / TOP2B
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) / 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 ...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) / 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 / neuron migration / cellular response to hydrogen peroxide / cellular senescence / ribonucleoprotein complex / chromatin binding / nucleolus / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol
Similarity search - Function
DTHCT / DTHCT (NUC029) region / DNA topoisomerase 2, TOPRIM domain / DNA topoisomerase II, eukaryotic-type / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / 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 ...DTHCT / DTHCT (NUC029) region / DNA topoisomerase 2, TOPRIM domain / DNA topoisomerase II, eukaryotic-type / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / 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
ADENOSINE-5'-DIPHOSPHATE / DNA topoisomerase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.621 Å
AuthorsLing, E.M. / Basle, A. / Cowell, I.G. / Blower, T.R. / Austin, C.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2022
Title: A comprehensive structural analysis of the ATPase domain of human DNA topoisomerase II beta bound to AMPPNP, ADP, and the bisdioxopiperazine, ICRF193.
Authors: Ling, E.M. / Basle, A. / Cowell, I.G. / van den Berg, B. / Blower, T.R. / Austin, C.A.
History
DepositionDec 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Mar 1, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Source and taxonomy
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_PDB_caveat / entity_src_gen / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _entity_src_gen.gene_src_common_name / _pdbx_nonpoly_scheme.auth_seq_num ..._entity_src_gen.gene_src_common_name / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.dist / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.R_factor_all / _refine_ls_shell.pdbx_fsc_free / _refine_ls_shell.pdbx_fsc_work / _refine_ls_shell.wR_factor_R_work / _software.version / _struct_conn.pdbx_dist_value
Description: Chirality error / Provider: author / Type: Coordinate replacement
Revision 2.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA topoisomerase 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5825
Polymers45,9381
Non-polymers6444
Water23413
1
A: DNA topoisomerase 2-beta
hetero molecules

A: DNA topoisomerase 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,16310
Polymers91,8762
Non-polymers1,2878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6800 Å2
ΔGint-112 kcal/mol
Surface area31210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.021, 103.021, 66.693
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

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


Mass: 45937.906 Da / Num. of mol.: 1
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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulphate, 0.1 M bis tris (pH 5.5), 25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.62→89.22 Å / Num. obs: 12596 / % possible obs: 100 % / Redundancy: 10.8 % / CC1/2: 0.997 / Net I/σ(I): 9
Reflection shellResolution: 2.62→2.74 Å / Redundancy: 11 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1513 / CC1/2: 0.78 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
xia2data reduction
MolProbitymodel building
pointlessdata scaling
Cootmodel building
Aimlessdata scaling
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292119290

Resolution: 2.621→89.219 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.179 / SU B: 32.249 / SU ML: 0.3 / Average fsc free: 0.9473 / Average fsc work: 0.9677 / Cross valid method: FREE R-VALUE / ESU R: 1.673 / ESU R Free: 0.34
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2588 540 4.292 %
Rwork0.1993 12043 -
all0.202 --
obs-12583 99.929 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 60.189 Å2
Baniso -1Baniso -2Baniso -3
1-1.796 Å20.898 Å20 Å2
2--1.796 Å2-0 Å2
3----5.826 Å2
Refinement stepCycle: LAST / Resolution: 2.621→89.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 38 13 2937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122981
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162747
X-RAY DIFFRACTIONr_angle_refined_deg1.9351.6464024
X-RAY DIFFRACTIONr_angle_other_deg0.6411.576419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2565357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.812511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.25110549
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.09910134
X-RAY DIFFRACTIONr_chiral_restr0.0830.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023270
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02579
X-RAY DIFFRACTIONr_nbd_refined0.2360.2617
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.22689
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21443
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0940.21642
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0320.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0040.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1480.216
X-RAY DIFFRACTIONr_nbd_other0.190.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3580.22
X-RAY DIFFRACTIONr_mcbond_it4.3984.5741437
X-RAY DIFFRACTIONr_mcbond_other4.3964.5751436
X-RAY DIFFRACTIONr_mcangle_it6.2426.8461791
X-RAY DIFFRACTIONr_mcangle_other6.2436.8471792
X-RAY DIFFRACTIONr_scbond_it5.2155.051544
X-RAY DIFFRACTIONr_scbond_other5.1795.0441536
X-RAY DIFFRACTIONr_scangle_it7.5767.3622233
X-RAY DIFFRACTIONr_scangle_other7.5577.3532222
X-RAY DIFFRACTIONr_lrange_it9.42455.3093335
X-RAY DIFFRACTIONr_lrange_other9.42355.3023336
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.621-2.6890.306460.3018650.3029130.9240.9399.78090.278
2.689-2.7620.354460.2798430.2838910.9190.94399.77550.263
2.762-2.8420.319130.2558620.2568760.9360.95699.88580.232
2.842-2.930.358390.2438170.2488570.8960.96199.88330.222
2.93-3.0260.368380.2337710.2388090.9340.9641000.21
3.026-3.1320.273460.2367490.2397950.9470.9641000.206
3.132-3.250.326250.2257290.2297540.9340.9661000.194
3.25-3.3820.307310.2127030.2167340.9280.971000.189
3.382-3.5320.211330.1856950.1867280.9660.9791000.165
3.532-3.7050.226230.176540.1726770.9680.9831000.153
3.705-3.9050.252240.1586190.1626430.9610.9851000.141
3.905-4.1410.222280.1555900.1586180.9710.9851000.137
4.141-4.4260.235210.145560.1435770.9720.9881000.13
4.426-4.780.182260.1525250.1545510.9810.9861000.142
4.78-5.2350.172210.1614730.1614940.980.9861000.153
5.235-5.850.278280.1834330.194630.9660.97999.5680.168
5.85-6.750.235190.2123920.2134110.9860.9731000.198
6.75-8.2550.313150.1943320.1983470.9510.9751000.189
8.255-11.6250.288100.2032700.2062800.9710.9741000.202
11.625-89.2190.25780.351650.3461740.980.93799.42530.353
Refinement TLS params.Method: refined / Origin x: 24.1147 Å / Origin y: 28.7573 Å / Origin z: 15.0194 Å
111213212223313233
T0.026 Å20.0169 Å20.0095 Å2-0.0611 Å20.0195 Å2--0.0424 Å2
L1.2156 °20.6744 °20.3695 °2-1.5242 °20.1786 °2--1.3959 °2
S0.0017 Å °0.0277 Å °0.1795 Å °-0.0513 Å °-0.0172 Å °0.1169 Å °-0.1433 Å °0.0543 Å °0.0155 Å °
Refinement TLS groupSelection: ALL

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