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

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Basic information

Entry
Database: PDB / ID: 5zen
TitleCrystal structure of human topoisomerase II beta in complex with DNA: a new quaternary conformation showing opening of the protein-linked DNA-gate
Components
  • DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
  • DNA (5'-D(P*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')
  • DNA topoisomerase 2-beta
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 / 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) / positive regulation of double-strand break repair via nonhomologous end joining / cellular response to ATP / 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 / nucleus / metal ion binding / 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 / 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 topoisomerase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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
DepositionFeb 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 (5'-D(P*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2075
Polymers97,0973
Non-polymers1102
Water34219
1
A: DNA topoisomerase 2-beta
B: DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
C: DNA (5'-D(P*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)194,41310
Polymers194,1946
Non-polymers2204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area10680 Å2
ΔGint-93 kcal/mol
Surface area64330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.760, 95.760, 231.055
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 chain DNA (5'-D(P*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')


Mass: 2731.798 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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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: 3.15 Å3/Da / Density % sol: 60.95 %
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: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→20 Å / Num. obs: 32586 / % possible obs: 99.6 % / Redundancy: 6.4 % / CC1/2: 0.983 / Net I/σ(I): 33.3
Reflection shellResolution: 2.75→2.85 Å / Rmerge(I) obs: 0.483 / CC1/2: 0.913

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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: 2.75→19.97 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.08
RfactorNum. reflection% reflection
Rfree0.266 2006 6.17 %
Rwork0.221 --
obs0.224 32531 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.75→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5361 349 2 19 5731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075905
X-RAY DIFFRACTIONf_angle_d0.7828095
X-RAY DIFFRACTIONf_dihedral_angle_d12.9693454
X-RAY DIFFRACTIONf_chiral_restr0.05923
X-RAY DIFFRACTIONf_plane_restr0.006983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7507-2.81930.28851390.28542136X-RAY DIFFRACTION99
2.8193-2.89530.36441360.28472120X-RAY DIFFRACTION100
2.8953-2.98020.36011370.28222173X-RAY DIFFRACTION100
2.9802-3.07610.32531430.2952137X-RAY DIFFRACTION100
3.0761-3.18560.35171400.27912153X-RAY DIFFRACTION100
3.1856-3.31260.29361420.26862172X-RAY DIFFRACTION100
3.3126-3.46260.3391410.25282154X-RAY DIFFRACTION100
3.4626-3.64410.26851450.23142158X-RAY DIFFRACTION100
3.6441-3.87090.24741420.21482171X-RAY DIFFRACTION100
3.8709-4.16720.27121450.19832206X-RAY DIFFRACTION100
4.1672-4.5820.20911430.18942179X-RAY DIFFRACTION100
4.582-5.23460.21641430.19052210X-RAY DIFFRACTION100
5.2346-6.55610.28391490.22982234X-RAY DIFFRACTION100
6.5561-19.97090.24721610.19472322X-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)
12.5503-1.047-1.18093.75050.72234.2505-0.16880.0012-0.3985-0.0608-0.08180.31210.57820.010.3360.4683-0.0077-0.02940.61990.01670.358638.8486-32.8734-58.0484
29.0778-1.7817-0.14936.7488-4.54067.808-0.43990.2333-1.14620.82480.1203-0.03270.81971.7280.2150.71940.23120.02650.7580.08530.502650.9125-32.4082-37.8601
32.6443-0.48920.23633.72-0.06152.8877-0.8882-0.3746-0.01670.36690.69620.06951.83151.00420.55560.75450.18760.05770.74050.14850.474550.3643-36.5619-49.9774
41.2878-0.3132-0.63384.08092.83353.58120.11430.09150.0558-0.1983-0.1215-0.3330.40180.10940.11510.47920.01350.04990.62870.08020.400247.5306-26.619-52.8633
52.02170.42210.79473.33851.48720.8344-0.1211-0.6412-0.2445-0.9642-0.0050.165-0.48520.53670.6160.64880.0090.11641.01690.01110.527157.8832-27.7039-54.6761
65.5535-5.07123.86134.611-3.70883.78180.45391.3241-0.4155-0.6049-1.22410.112-0.1291-0.05840.61160.61770.11260.03850.82610.08740.382445.1047-22.1506-58.9836
71.6098-1.486-2.84074.92661.72545.24440.1606-1.2407-0.7892-1.02120.00650.685-0.7496-1.28780.0770.9009-0.1101-0.1221.266-0.11980.763527.4284-20.0627-56.6337
87.8095-2.5018-3.34263.5243.33453.39520.9519-0.67891.0047-0.017-1.49670.53390.58950.27060.64161.3418-0.1318-0.23442.1065-0.08930.979130.5966-21.31-65.8607
91.5377-0.24761.07493.5287-0.75793.00520.03921.54090.4964-0.1362-0.35790.0009-0.1440.80440.04070.80170.06330.16791.17960.11410.685548.0995-18.4851-62.219
100.2379-1.08920.12057.82062.64073.6147-0.49321.1571-0.65390.2131-0.1099-1.00910.78891.1720.73030.5367-0.03980.15071.16280.14160.504356.7234-16.7883-45.5773
118.3256-4.26040.61786.2472.40111.7090.46260.28421.4258-1.901-0.5515-0.89180.03280.46130.43470.6856-0.1364-0.01430.82360.1320.731849.8399-3.7015-40.7708
120.1283-0.75250.41781.79010.57251.85420.09870.42870.2189-0.3585-0.2420.0284-0.217-0.13050.19890.4193-0.07960.00120.71590.08710.440543.1632-9.9083-43.0383
131.2292-0.16051.3573.28230.44114.22170.10690.0255-0.1234-0.325-0.05240.30870.1539-0.2560.01050.2986-0.116-0.0350.48050.00570.43921.397-13.9533-29.8168
144.1595-2.84151.56568.84981.65953.23090.56090.0658-0.8139-0.0449-0.53350.86810.5839-0.26980.0260.4714-0.20580.01530.51370.06080.475820.9697-22.2745-23.8829
152.3328-0.54570.73570.48370.43581.4832-0.57780.3891-0.02150.0569-0.1903-0.7363-0.67380.44790.76430.32670.0504-0.06320.4972-0.0360.550620.22632.6894-25.326
163.34780.34650.35063.86632.57932.1707-0.26181.16830.4573-0.6296-0.28860.3423-0.92310.20140.54950.505-0.1207-0.1690.71010.13670.692425.69041.3377-36.0559
171.9206-1.6499-0.18371.9661-0.1233.0025-0.14530.09030.04020.3284-0.1263-0.1127-0.03930.24650.24920.375-0.1207-0.03550.55380.00880.520835.1019-3.825-17.4026
180.6785-1.5121-0.21237.5207-1.2221.68910.1661-0.31850.17852.1506-0.3326-0.2605-0.3790.35580.12430.5845-0.1484-0.15380.53160.0150.493737.7691-7.6449-7.9488
194.49522.9299-3.58653.686-4.23868.4589-0.14150.22940.08090.3805-0.0603-0.3045-0.25680.10580.20270.4249-0.1023-0.06130.53250.00460.409340.3592-23.8524-0.7972
203.5617-2.60520.87258.719-1.46064.9072-0.02970.6204-0.193-0.7724-0.3821-0.26510.78330.16830.26660.5274-0.11390.07750.42280.04250.357436.6516-31.2944-9.8927
211.465-1.40671.13682.74470.26049.1878-0.41330.87890.1298-0.3994-0.10420.09281.43620.84360.21230.72610.0259-0.03460.7290.03810.569639.8937-40.6826-5.4017
224.5262-2.68111.42254.4494-1.84062.9104-0.0667-0.1658-0.01610.29770.01560.07040.0020.1270.02320.6047-0.1216-0.01060.46690.01760.412239.1645-32.56120.2048
232.15810.2607-0.53142.1875-0.38650.275-0.08470.2890.60870.4608-0.3159-0.9439-0.47490.41130.38290.4136-0.134-0.04690.62710.07010.520443.3774-7.3324-20.5058
242.8818-0.08481.393-0.1655-1.04350.8212-0.254-1.11490.7607-0.36570.27520.4016-0.5-0.36990.18870.86750.1248-0.37110.3952-0.13111.214710.908319.7955-31.7189
252.5468-3.2928-0.59465.5472-1.91926.0418-0.2767-0.81290.769-1.1196-0.11271.6240.430.45880.4150.87770.1143-0.64430.545-0.04121.538210.812122.1948-38.7966
262.21371.60651.10445.0205-0.65674.7734-0.6912-0.18910.0470.1394-0.9840.7744-1.4487-0.99161.13191.1360.301-0.75210.2493-0.04041.7379-4.109719.6537-38.5662
273.8912-0.83783.18881.2009-0.35642.8534-0.7952-0.49070.81750.19280.4020.1132-0.4742-0.65140.47480.51820.0315-0.08490.6052-0.11530.827512.92119.0747-16.404
284.3278-1.43143.80581.3988-2.40144.74420.22550.24241.0889-0.60790.07771.1451-0.808-0.4335-0.44511.00840.3666-0.10941.82850.00590.81130.7564-9.6161-59.336
290.927-0.99380.03563.565-1.17160.5276-0.0192-0.16980.8107-0.9421.1691-1.07110.3235-0.1847-0.47341.46120.1239-0.12730.99860.24611.401434.7882-8.4632-61.4067
301.0946-0.72182.04680.5275-1.29773.8383-0.923-0.44980.72450.3047-0.5760.4516-1.1282-0.66391.06961.8710.3097-0.22161.4668-0.12261.633734.1016-0.7527-58.0516
314.53182.4265-2.41493.55611.7415.3721.10250.0079-1.14770.3362-0.0998-1.01-0.35920.1123-0.34761.13420.1338-0.24881.81620.2851.186226.5439-10.3473-56.1441
327.7469-5.0261-0.24284.3676-2.52027.072-0.01371.5510.62080.727-0.37420.4772-1.21340.16640.79671.1950.2068-0.16120.9461-0.06881.052343.3655-4.9671-56.1422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 452 THROUGH 508 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 509 THROUGH 520 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 521 THROUGH 538 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 540 THROUGH 576 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 577 THROUGH 583 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 584 THROUGH 591 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 632 THROUGH 636 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 637 THROUGH 645 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 646 THROUGH 658 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 659 THROUGH 670 )
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 671 THROUGH 696 )
12X-RAY DIFFRACTION12CHAIN 'A' AND (RESID 707 THROUGH 739 )
13X-RAY DIFFRACTION13CHAIN 'A' AND (RESID 740 THROUGH 808 )
14X-RAY DIFFRACTION14CHAIN 'A' AND (RESID 809 THROUGH 828 )
15X-RAY DIFFRACTION15CHAIN 'A' AND (RESID 829 THROUGH 841 )
16X-RAY DIFFRACTION16CHAIN 'A' AND (RESID 842 THROUGH 861 )
17X-RAY DIFFRACTION17CHAIN 'A' AND (RESID 862 THROUGH 897 )
18X-RAY DIFFRACTION18CHAIN 'A' AND (RESID 898 THROUGH 919 )
19X-RAY DIFFRACTION19CHAIN 'A' AND (RESID 920 THROUGH 936 )
20X-RAY DIFFRACTION20CHAIN 'A' AND (RESID 937 THROUGH 961 )
21X-RAY DIFFRACTION21CHAIN 'A' AND (RESID 962 THROUGH 976 )
22X-RAY DIFFRACTION22CHAIN 'A' AND (RESID 978 THROUGH 1004 )
23X-RAY DIFFRACTION23CHAIN 'A' AND (RESID 1005 THROUGH 1032 )
24X-RAY DIFFRACTION24CHAIN 'A' AND (RESID 1033 THROUGH 1095 )
25X-RAY DIFFRACTION25CHAIN 'A' AND (RESID 1096 THROUGH 1111 )
26X-RAY DIFFRACTION26CHAIN 'A' AND (RESID 1135 THROUGH 1150 )
27X-RAY DIFFRACTION27CHAIN 'A' AND (RESID 1151 THROUGH 1201 )
28X-RAY DIFFRACTION28CHAIN 'A' AND (RESID 592 THROUGH 596 )
29X-RAY DIFFRACTION29CHAIN 'A' AND (RESID 603 THROUGH 607 )
30X-RAY DIFFRACTION30CHAIN 'A' AND (RESID 608 THROUGH 615 )
31X-RAY DIFFRACTION31CHAIN 'A' AND (RESID 625 THROUGH 631 )
32X-RAY DIFFRACTION32CHAIN 'A' AND (RESID 697 THROUGH 702 )

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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