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- PDB-3qx3: Human topoisomerase IIbeta in complex with DNA and etoposide -

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Basic information

Entry
Database: PDB / ID: 3qx3
TitleHuman topoisomerase IIbeta in complex with DNA and etoposide
Components
  • DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
  • DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')
  • DNA topoisomerase 2-beta
KeywordsISOMERASE/DNA/ISOMERASE INHIBITOR / TOPRIM domain / winged-helix domain / coiled-coil domain / DNA binding and cleavage / nucleus / ISOMERASE-DNA-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 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 / axonogenesis / B cell differentiation / neuron migration / cellular response to hydrogen peroxide / cellular senescence / ribonucleoprotein complex / chromatin binding / nucleolus / DNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / DTHCT / DTHCT (NUC029) region / Topoisomerase, domain 3 / Topoisomerase; domain 3 / DNA topoisomerase 2, TOPRIM domain / Rossmann fold - #670 / Gyrase A; domain 2 - #40 / DNA topoisomerase II, eukaryotic-type ...Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / DTHCT / DTHCT (NUC029) region / Topoisomerase, domain 3 / Topoisomerase; domain 3 / DNA topoisomerase 2, TOPRIM domain / Rossmann fold - #670 / Gyrase A; domain 2 - #40 / 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 / Gyrase A; domain 2 / 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 / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-EVP / DNA / DNA (> 10) / DNA topoisomerase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.162 Å
AuthorsWu, C.C. / Li, T.K. / Farh, L. / Lin, L.Y. / Lin, T.S. / Yu, Y.J. / Yen, T.J. / Chiang, C.W. / Chan, N.L.
CitationJournal: Science / Year: 2011
Title: Structural basis of type II topoisomerase inhibition by the anticancer drug etoposide
Authors: Wu, C.C. / Li, T.K. / Farh, L. / Lin, L.Y. / Lin, T.S. / Yu, Y.J. / Yen, T.J. / Chiang, C.W. / Chan, N.L.
History
DepositionMar 1, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 25, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 2-beta
B: DNA topoisomerase 2-beta
C: DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
D: DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')
E: DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
F: DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,36214
Polymers196,0396
Non-polymers1,3238
Water18,8621047
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12490 Å2
ΔGint-70 kcal/mol
Surface area64430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.149, 176.801, 94.067
Angle α, β, γ (deg.)90.00, 111.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 91928.367 Da / Num. of mol.: 2 / Fragment: hTOP2beta cleavage core, UNP residues 450-1206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOP2B / Plasmid: pET51b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21star(DE3) / References: UniProt: Q02880, EC: 5.99.1.3

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DNA chain , 2 types, 4 molecules CEDF

#2: DNA chain DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')


Mass: 2436.619 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The oligonucleotide sequence 5'-AGCCGAGCTGCAGCTCGGCT-3' was purchased from VIOGENE.
#3: DNA chain DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')


Mass: 3654.378 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The oligonucleotide sequence 5'-AGCCGAGCTGCAGCTCGGCT-3' was purchased from VIOGENE.

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Non-polymers , 3 types, 1055 molecules

#4: Chemical ChemComp-EVP / (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside / Etoposide / VP-16 / Etoposide


Mass: 588.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H32O13 / Comment: medication, chemotherapy*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1047 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE OF DNA USED IN THE EXPERIMENT WAS 5'-AGCCGAGCTGCAGCTCGGCT-3'. AND THE DNAS WERE ...THE SEQUENCE OF DNA USED IN THE EXPERIMENT WAS 5'-AGCCGAGCTGCAGCTCGGCT-3'. AND THE DNAS WERE CLEAVED INTO TWO PIECES (TOTALLY 4 STRANDS, DESIGNATED AS CHAIN C, D, E AND F) DURING EXPERIMENT.

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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: 3.16 Å3/Da / Density % sol: 61.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.1M magnesium acetate, 50mM 2-(N-morpholino)ethanesulfonic acid pH 5.8, 22% 2-methyl-2, 4-pentanediol (MPT), VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 2, 2010
RadiationMonochromator: Fixed-Exit Double Crystal Monochromator (Crystal type Si(1 1 1))
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.16→30 Å / Num. all: 123847 / Num. obs: 129411 / % possible obs: 95.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Biso Wilson estimate: 32.09 Å2 / Rsym value: 0.06 / Net I/σ(I): 16.9
Reflection shellResolution: 2.16→2.2 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.472 / % possible all: 98.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.automr: 1.6.4_486)model building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.6.4_486phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L4K

3l4k


Resolution: 2.162→29.543 Å / FOM work R set: 0.8652 / SU ML: 0.25 / σ(F): 0 / Phase error: 21.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2072 5917 5.03 %
Rwork0.1682 --
obs0.1701 117720 90.82 %
all-129619 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso mean: 37.0272 Å2
Baniso -1Baniso -2Baniso -3
1-6.3155 Å2-0 Å25.9953 Å2
2--1.0717 Å2-0 Å2
3---3.9119 Å2
Refinement stepCycle: LAST / Resolution: 2.162→29.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10826 820 90 1047 12783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712326
X-RAY DIFFRACTIONf_angle_d1.05816825
X-RAY DIFFRACTIONf_dihedral_angle_d15.4424791
X-RAY DIFFRACTIONf_chiral_restr0.0691857
X-RAY DIFFRACTIONf_plane_restr0.0042017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1619-2.23910.28825720.232510113X-RAY DIFFRACTION82
2.2391-2.32880.26895370.209710652X-RAY DIFFRACTION87
2.3288-2.43470.24825760.194511012X-RAY DIFFRACTION90
2.4347-2.5630.23165760.190211223X-RAY DIFFRACTION91
2.563-2.72350.23575740.178111420X-RAY DIFFRACTION93
2.7235-2.93360.21316300.171211577X-RAY DIFFRACTION94
2.9336-3.22850.21816520.165611605X-RAY DIFFRACTION95
3.2285-3.69490.18955940.151311700X-RAY DIFFRACTION95
3.6949-4.65220.16866250.139711317X-RAY DIFFRACTION92
4.6522-29.54620.19825810.172611184X-RAY DIFFRACTION90

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