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- PDB-5gwk: Human topoisomerase IIalpha in complex with DNA and etoposide -

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Basic information

Entry
Database: PDB / ID: 5gwk
TitleHuman topoisomerase IIalpha 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-alpha
KeywordsISOMERASE/DNA/ISOMERASE INHIBITOR / Type II topoisomerase / Anti-cancer drug / TopoII cleavage complex / ISOMERASE-DNA-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
Dna Ligase; domain 1 - #30 / Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / DTHCT / DTHCT (NUC029) region / DNA topoisomerase 2, TOPRIM domain / Rossmann fold - #670 / Gyrase A; domain 2 - #40 ...Dna Ligase; domain 1 - #30 / Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / DTHCT / DTHCT (NUC029) region / DNA topoisomerase 2, TOPRIM domain / Rossmann fold - #670 / Gyrase A; domain 2 - #40 / 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 / Gyrase A; domain 2 / Dna Ligase; domain 1 / 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-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.152 Å
AuthorsWang, Y.R. / Wu, C.C. / Chan, N.L.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry
Authors: Wang, Y.R. / Chen, S.F. / Wu, C.C. / Liao, Y.W. / Lin, T.S. / Liu, K.T. / Chen, Y.S. / Li, T.K. / Chien, T.C. / Chan, N.L.
History
DepositionSep 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.country / _citation.journal_abbrev ..._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 / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.2Nov 8, 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 / struct_conn / struct_conn_type
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 / _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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
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)199,34014
Polymers198,0176
Non-polymers1,3238
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15050 Å2
ΔGint-120 kcal/mol
Surface area68600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.113, 126.155, 198.856
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

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


Mass: 92917.750 Da / Num. of mol.: 2 / Fragment: UNP residues 430-1188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOP2A, TOP2 / Plasmid: pET51b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11388, EC: 5.99.1.3
#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 / Source: (synth.) synthetic construct (others)
#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 / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: 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


Mass: 588.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H32O13 / Comment: medication, chemotherapy*YM
Has protein modificationY

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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: 3.51 Å3/Da / Density % sol: 64.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Magnesium Acetate, 2-(N-morpholino)ethanesulfonic acid, 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 3.15→27.488 Å / Num. obs: 45909 / % possible obs: 99.2 % / Redundancy: 6.7 % / Rsym value: 0.48 / Net I/σ(I): 24.6
Reflection shellResolution: 3.15→3.2 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data processing
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QX3

3qx3


Resolution: 3.152→27.488 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2437 2000 4.36 %
Rwork0.2028 --
obs0.2046 45898 99.14 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.152→27.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11760 820 90 0 12670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213032
X-RAY DIFFRACTIONf_angle_d0.56617754
X-RAY DIFFRACTIONf_dihedral_angle_d12.2155024
X-RAY DIFFRACTIONf_chiral_restr0.0231948
X-RAY DIFFRACTIONf_plane_restr0.0032114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1525-3.23120.3241390.25973054X-RAY DIFFRACTION98
3.2312-3.31840.31931420.25353110X-RAY DIFFRACTION100
3.3184-3.41590.29361420.253138X-RAY DIFFRACTION100
3.4159-3.5260.3341410.23383093X-RAY DIFFRACTION100
3.526-3.65170.29541430.24323128X-RAY DIFFRACTION100
3.6517-3.79760.29771430.23353130X-RAY DIFFRACTION100
3.7976-3.96990.22191420.22813126X-RAY DIFFRACTION100
3.9699-4.17850.27171430.20313129X-RAY DIFFRACTION100
4.1785-4.43930.22891430.19353151X-RAY DIFFRACTION100
4.4393-4.78040.21811440.18963164X-RAY DIFFRACTION100
4.7804-5.25850.24061450.19453177X-RAY DIFFRACTION100
5.2585-6.01240.26981440.2093163X-RAY DIFFRACTION100
6.0124-7.5490.22591470.19553225X-RAY DIFFRACTION100
7.549-27.48930.18291420.16273110X-RAY DIFFRACTION92

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