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- PDB-8ke7: Crystal structure of DNA binding and cleavage core of human topoi... -

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Basic information

Entry
Database: PDB / ID: 8ke7
TitleCrystal structure of DNA binding and cleavage core of human topoisomerase 2-beta in a DNA binding-competent conformation
ComponentsDNA topoisomerase 2-beta
KeywordsDNA BINDING PROTEIN / eukaryotic DNA topoisomerase G-segment DNA binding cleavage center assembly
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 / positive regulation of double-strand break repair via nonhomologous end joining / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / cellular response to ATP / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / SUMOylation of DNA replication proteins / forebrain development ...positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / resolution of meiotic recombination intermediates / positive regulation of double-strand break repair via nonhomologous end joining / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / cellular response to ATP / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / SUMOylation of DNA replication proteins / forebrain development / 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
DTHCT / DTHCT (NUC029) region / DNA topoisomerase 2, TOPRIM domain / 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 ...DTHCT / DTHCT (NUC029) region / DNA topoisomerase 2, TOPRIM domain / 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 / 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
Similarity search - Domain/homology
ACETATE ION / DNA topoisomerase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChan, N.L. / Liu, K.T. / Chen, S.F.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan) Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structural insights into the assembly of type IIA topoisomerase DNA cleavage-religation center.
Authors: Liu, K.T. / Chen, S.F. / Chan, N.L.
History
DepositionAug 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA topoisomerase 2-beta
B: DNA topoisomerase 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,38811
Polymers183,8572
Non-polymers5319
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint-25 kcal/mol
Surface area61710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.719, 113.708, 209.267
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 449 through 469 or (resid 470...
d_2ens_1(chain "B" and (resid 449 or (resid 450 through 452...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERTHRTHRAA449 - 70431 - 286
d_12THRTHRLEULEUAA706 - 780288 - 362
d_13METMETVALVALAA782 - 889364 - 471
d_14ASNASNASNASNAA891 - 961473 - 543
d_15ALAALALYSLYSAA968 - 1086550 - 668
d_16ASPASPGLNGLNAA1088 - 1091670 - 673
d_17LEULEUGLYGLYAA1093 - 1202675 - 784
d_21SERSERLEULEUBB449 - 78031 - 362
d_22METMETVALVALBB782 - 889364 - 471
d_23ASNASNLYSLYSBB891 - 1086473 - 668
d_24ASPASPGLNGLNBB1088 - 1091670 - 673
d_25LEULEUGLYGLYBB1093 - 1202675 - 784

NCS oper: (Code: givenMatrix: (-0.989911645281, 0.0202387288177, 0.140233121594), (0.0197399308558, -0.960392462062, 0.277950812094), (0.140304204021, 0.277914937831, 0.950304171129)Vector: 45. ...NCS oper: (Code: given
Matrix: (-0.989911645281, 0.0202387288177, 0.140233121594), (0.0197399308558, -0.960392462062, 0.277950812094), (0.140304204021, 0.277914937831, 0.950304171129)
Vector: 45.1034974542, -9.21542191766, -1.88363469002)

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Components

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


Mass: 91928.367 Da / Num. of mol.: 2
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, EC: 5.99.1.3
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.26 Å3/Da / Density % sol: 62.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium acetate, calcium chloride dehydrate, sodium cacodylate trihydrate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→19.83 Å / Num. obs: 58573 / % possible obs: 99.6 % / Redundancy: 4.8 % / Biso Wilson estimate: 55.27 Å2 / Rpim(I) all: 0.064 / Rrim(I) all: 0.141 / Net I/σ(I): 11.69
Reflection shellResolution: 2.84→2.94 Å / Num. unique obs: 5768 / CC1/2: 0.756

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.83 Å / SU ML: 0.3726 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0008
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2381 2000 3.42 %
Rwork0.1937 56510 -
obs0.1952 58510 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.67 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11445 0 36 144 11625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411746
X-RAY DIFFRACTIONf_angle_d0.810915869
X-RAY DIFFRACTIONf_chiral_restr0.0551753
X-RAY DIFFRACTIONf_plane_restr0.00572054
X-RAY DIFFRACTIONf_dihedral_angle_d19.33781571
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.713755707602 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.39281170.30533283X-RAY DIFFRACTION80.66
2.87-2.950.33151420.27864030X-RAY DIFFRACTION100
2.95-3.040.30671440.264068X-RAY DIFFRACTION99.98
3.04-3.130.31461430.24894047X-RAY DIFFRACTION99.98
3.13-3.250.30011450.24554083X-RAY DIFFRACTION99.91
3.25-3.370.25511430.22614061X-RAY DIFFRACTION99.86
3.37-3.530.28461440.21624073X-RAY DIFFRACTION99.95
3.53-3.710.26911450.21524093X-RAY DIFFRACTION99.86
3.71-3.940.24291450.19724091X-RAY DIFFRACTION100
3.94-4.240.19251440.16554092X-RAY DIFFRACTION99.84
4.24-4.670.19741470.14664105X-RAY DIFFRACTION99.72
4.67-5.330.20961460.15564137X-RAY DIFFRACTION99.4
5.33-6.670.21541480.18784196X-RAY DIFFRACTION99.95
6.67-19.830.18761470.16234151X-RAY DIFFRACTION95.77
Refinement TLS params.Method: refined / Origin x: 25.459178797 Å / Origin y: 0.779163431208 Å / Origin z: 38.3662268254 Å
111213212223313233
T0.284781616907 Å2-0.00360666721014 Å20.00843051671671 Å2-0.440023811247 Å20.101596029611 Å2--0.42824763273 Å2
L0.520113166544 °20.0550524994613 °20.0141521578993 °2-0.555143603169 °20.26438370556 °2--0.45122084321 °2
S-0.0533889768589 Å °0.1593975772 Å °0.0320458829585 Å °-0.127223032907 Å °0.0233224416482 Å °0.101613306157 Å °-0.0867206001707 Å °-0.0454497544264 Å °0.0314601963787 Å °
Refinement TLS groupSelection details: all

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