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- PDB-5zqf: Crystal structure of human topoisomerase II beta in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5zqf
TitleCrystal structure of human topoisomerase II beta in complex with 5-iodouridine-containing-DNA in space group P3221
Components
  • DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
  • DNA topoisomerase 2-beta
  • DNA/RNA (5'-D(P*AP*GP*C)-R(P*(IU))-D(P*CP*GP*GP*C)-R(P*(IU))-3')
KeywordsISOMERASE/DNA / Type II topoisomerase / cleavage complex / DNA-gate / 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 / 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
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
: / DNA / DNA/RNA hybrid / DNA topoisomerase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.873 Å
AuthorsChen, S.F. / Wang, Y.R. / Chan, N.L.
CitationJournal: Nat Commun / Year: 2018
Title: Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate.
Authors: Chen, S.F. / Huang, N.L. / Lin, J.H. / Wu, C.C. / Wang, Y.R. / Yu, Y.J. / Gilson, M.K. / Chan, N.L.
History
DepositionApr 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Nov 22, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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 (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
C: DNA/RNA (5'-D(P*AP*GP*C)-R(P*(IU))-D(P*CP*GP*GP*C)-R(P*(IU))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4625
Polymers97,3533
Non-polymers1102
Water00
1
A: DNA topoisomerase 2-beta
B: DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
C: DNA/RNA (5'-D(P*AP*GP*C)-R(P*(IU))-D(P*CP*GP*GP*C)-R(P*(IU))-3')
hetero molecules

A: DNA topoisomerase 2-beta
B: DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
C: DNA/RNA (5'-D(P*AP*GP*C)-R(P*(IU))-D(P*CP*GP*GP*C)-R(P*(IU))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,92510
Polymers194,7056
Non-polymers2204
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area12930 Å2
ΔGint-80 kcal/mol
Surface area63830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.990, 94.990, 231.486
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 91928.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOP2B / Plasmid: pET51b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (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.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA/RNA hybrid DNA/RNA (5'-D(P*AP*GP*C)-R(P*(IU))-D(P*CP*GP*GP*C)-R(P*(IU))-3')


Mass: 2987.538 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn

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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: 3.1 Å3/Da / Density % sol: 60.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Magnesium Acetate, 2-(N-morpholino)ethanesulfonic, 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.87→30 Å / Num. obs: 11767 / % possible obs: 99.2 % / Redundancy: 6.7 % / CC1/2: 0.97 / Net I/σ(I): 14.1
Reflection shellResolution: 3.87→4.01 Å / Rmerge(I) obs: 0.696

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QX3

3qx3


Resolution: 3.873→19.904 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2474 1178 10.04 %
Rwork0.203 --
obs0.2075 11734 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.873→19.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5353 351 2 0 5706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065891
X-RAY DIFFRACTIONf_angle_d0.5378075
X-RAY DIFFRACTIONf_dihedral_angle_d12.1253428
X-RAY DIFFRACTIONf_chiral_restr0.04918
X-RAY DIFFRACTIONf_plane_restr0.004981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8727-4.04750.30441430.25781289X-RAY DIFFRACTION100
4.0475-4.2590.26841420.22321299X-RAY DIFFRACTION100
4.259-4.52290.25861460.20471303X-RAY DIFFRACTION100
4.5229-4.86740.23221420.18121289X-RAY DIFFRACTION100
4.8674-5.34860.23471480.1971325X-RAY DIFFRACTION100
5.3486-6.10290.28631500.21911318X-RAY DIFFRACTION100
6.1029-7.61670.24031480.22191338X-RAY DIFFRACTION100
7.6167-19.90390.22151590.17681395X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.006-0.0768-0.06550.56170.57420.48120.0196-0.23140.3624-0.2669-0.0432-0.3375-1.35780.48620.00011.24880.08490.14211.1303-0.03220.8814-37.849733.5264-59.9658
23.05560.15720.64184.6996-0.76890.2722-1.05790.1319-0.2016-0.0831-1.00860.36780.18020.1884-0.66430.81220.1879-0.00771.9677-0.21320.6992-47.551926.4567-40.2783
30.4707-0.1530.2450.8572-0.91950.8189-0.1997-0.32290.0198-0.1007-0.0898-0.1076-0.5993-0.613600.81380.213-0.1011.012-0.15320.7855-49.171429.585-51.458
40.6420.4410.33070.32060.24590.17830.33740.1792-0.71460.07770.5182-0.6860.40261.152-0.00961.34260.34370.18062.1019-0.21361.2852-33.339313.2368-59.6213
50.01710.04450.11490.10660.2880.75840.2229-0.006-0.18680.48260.01951.208-0.0611-0.18960.0772.95540.1277-1.23810.9417-0.07843.0579-33.98988.3404-61.6102
60.0062-0-0.0120.01670.00140.0239-0.5133-0.59170.3169-0.0259-0.6488-0.2831-0.1646-0.2325-0.00113.11650.30550.63552.21110.2172.9882-33.50530.5986-58.0712
70.0103-0.0094-0.0358-00.02030.0808-0.4495-0.24350.33740.08910.18220.68550.1740.13770.00031.47770.1957-0.12511.6892-0.14641.7569-26.261413.5682-56.3072
80.0048-0.00520.00390.01250.01070.0153-0.4236-0.355-0.22740.2257-0.0727-0.1093-0.07780.3104-0.00032.5080.1734-0.04581.43330.26351.8132-29.904121.2571-65.7561
90.0354-0.21430.2590.5826-0.64060.5809-0.48860.3173-0.2291-0.0697-0.0631-0.66460.5713-0.9312-0.01421.17370.0410.021.2475-0.13580.8985-49.49939.6627-48.5574
100.2332-0.339-0.08440.84890.67610.6351-0.050.0607-0.2498-0.2291-0.0689-0.1788-0.039-0.2663-00.7999-0.08630.06351.00490.00630.9072-31.03459.8818-38.6872
110.43610.4784-0.59722.5637-0.6771.85660.0752-0.06570.05220.2165-0.1415-0.1322-0.24460.315900.5453-0.04750.01290.65980.02980.7673-27.29358.2248-23.115
120.5237-0.5527-0.75251.02-0.00051.35390.0125-0.0349-0.0117-0.0133-0.1440.1779-0.1445-0.141300.9826-0.1870.04990.8989-0.06450.8286-39.101629.647-4.7058
131.0541.10480.33851.09670.11621.6569-0.1979-0.0223-0.5745-0.4828-0.12560.3120.9225-0.1874-2.19451.117-0.1320.32620.66580.28380.9709-24.6745-11.0645-26.3177
142.2061-0.97151.4041.3991-0.10881.8193-0.1348-0.3039-1.6827-0.32690.0286-0.72450.23150.13440.58432.0050.0810.64180.6124-0.30482.2745-1.7113-25.8938-42.3516
15-0.0074-0.00560.01420.01670.05780.0576-1.28160.3254-0.2964-0.0687-0.7121-0.31911.0170.089-0.00511.92440.32480.58351.41840.13562.52584.6022-19.8057-38.4211
160.10380.0467-0.2868-0.0119-0.12060.2366-0.2791-0.55370.2025-0.02370.2381-0.3390.33840.48120.00011.17050.04750.1140.93830.19911.2367-12.2967-9.2134-16.3221
170.0101-0.01660.0518-0.00120.00530.0570.32130.14211.14220.04920.5037-0.1559-1.8593-0.36160.00061.37480.23920.28081.33370.05711.4515-38.531722.4307-30.1947
180.03660.05470.01670.03980.020.0346-0.5285-0.27351.27620.29690.2282-1.34380.04170.0790.00211.7677-0.37140.13492.1441-0.10641.5107-36.416530.4052-37.4482
19-0.01480.0053-0.0001-0.00930.00510.0266-0.3884-1.02591.39411.2991-0.57520.1399-0.8338-0.7018-0.00061.2411-0.43970.07181.3194-0.09251.0589-46.872517.1297-28.4946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 452 through 502 )
2X-RAY DIFFRACTION2chain 'A' and (resid 503 through 513 )
3X-RAY DIFFRACTION3chain 'A' and (resid 514 through 588 )
4X-RAY DIFFRACTION4chain 'A' and (resid 589 through 596 )
5X-RAY DIFFRACTION5chain 'A' and (resid 603 through 607 )
6X-RAY DIFFRACTION6chain 'A' and (resid 608 through 615 )
7X-RAY DIFFRACTION7chain 'A' and (resid 625 through 636 )
8X-RAY DIFFRACTION8chain 'A' and (resid 637 through 645 )
9X-RAY DIFFRACTION9chain 'A' and (resid 646 through 702 )
10X-RAY DIFFRACTION10chain 'A' and (resid 707 through 771 )
11X-RAY DIFFRACTION11chain 'A' and (resid 772 through 913 )
12X-RAY DIFFRACTION12chain 'A' and (resid 914 through 1012 )
13X-RAY DIFFRACTION13chain 'A' and (resid 1013 through 1076 )
14X-RAY DIFFRACTION14chain 'A' and (resid 1077 through 1111 )
15X-RAY DIFFRACTION15chain 'A' and (resid 1135 through 1150 )
16X-RAY DIFFRACTION16chain 'A' and (resid 1151 through 1201 )
17X-RAY DIFFRACTION17chain 'B' and (resid 1 through 8 )
18X-RAY DIFFRACTION18chain 'C' and (resid 12 through 14 )
19X-RAY DIFFRACTION19chain 'C' and (resid 16 through 19 )

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