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- PDB-4j3n: Human Topoisomerase Iibeta in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 4j3n
TitleHuman Topoisomerase Iibeta in complex with DNA
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 / TOPRIM DOMAIN / WINGED-HELIX DOMAIN / COILED-COIL DOMAIN / DNA BINDING AND CLEAVAGE / NUCLEUS / ISOMERASE-DNA 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) / positive regulation of double-strand break repair via nonhomologous end joining / cellular response to ATP / forebrain development / DNA topological change / SUMOylation of DNA replication proteins ...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) / positive regulation of double-strand break repair via nonhomologous end joining / cellular response to ATP / forebrain development / DNA topological change / SUMOylation of DNA replication proteins / ribonucleoprotein complex binding / axonogenesis / B cell differentiation / cellular response to hydrogen peroxide / neuron migration / 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 / 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 ...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 / Histidine kinase-, DNA gyrase B-, and 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
DNA / DNA (> 10) / DNA topoisomerase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWu, C.C. / Li, T.K. / Li, Y.C. / Chan, N.L.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: On the structural basis and design guidelines for type II topoisomerase-targeting anticancer drugs
Authors: Wu, C.C. / Li, Y.C. / Wang, Y.R. / Li, T.K. / Chan, N.L.
History
DepositionFeb 6, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)196,20913
Polymers196,0396
Non-polymers1707
Water12,665703
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13910 Å2
ΔGint-127 kcal/mol
Surface area63400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.953, 176.368, 94.225
Angle α, β, γ (deg.)90.00, 112.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#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 ORDERED 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 ORDERED FROM VIOGENE.
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 703 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 3.14 Å3/Da / Density % sol: 60.84 %
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: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 25, 2010
RadiationMonochromator: HORIZONTALLY FOCUSING SINGLE CRYSTAL MONOCHROMATOR (CRYSTAL TYPE SI(1 1 1))
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 109988 / Num. obs: 103829 / % possible obs: 94.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rsym value: 0.06 / Net I/σ(I): 13.4
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5259 / Rsym value: 0.489 / % possible all: 94.4

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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: 2.3→27.31 Å / Occupancy max: 1 / Occupancy min: 0.12 / SU ML: 0.28 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.218 4954 4.99 %Random
Rwork0.176 ---
all0.178 106932 --
obs0.178 99340 92.9 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.53 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso max: 139.83 Å2 / Biso mean: 46.3339 Å2 / Biso min: 18.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.3477 Å2-0 Å26.7788 Å2
2---5.0532 Å2-0 Å2
3---2.7055 Å2
Refinement stepCycle: LAST / Resolution: 2.3→27.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10783 799 7 703 12292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712110
X-RAY DIFFRACTIONf_angle_d1.08216477
X-RAY DIFFRACTIONf_dihedral_angle_d16.0864699
X-RAY DIFFRACTIONf_chiral_restr0.0681816
X-RAY DIFFRACTIONf_plane_restr0.0041988
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3001-2.38230.28194210.2273857384
2.3823-2.47760.26944520.209898389
2.4776-2.59030.25414660.2046925191
2.5903-2.72670.26125190.2003942093
2.7267-2.89740.25065420.1958955895
2.8974-3.12080.24615050.1917968195
3.1208-3.43430.22715020.1743977396
3.4343-3.930.19465130.1569980396
3.93-4.94660.17595030.1452978896
4.9466-27.31230.20575310.1812955693

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