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- PDB-3l4j: Topoisomerase II-DNA cleavage complex, apo -

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Basic information

Entry
Database: PDB / ID: 3l4j
TitleTopoisomerase II-DNA cleavage complex, apo
Components
  • DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)-3')
  • DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)-3')
  • DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3')
  • DNA (5'-D(P*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*)-3')
  • DNA topoisomerase 2Topoisomerase
KeywordsIsomerase/DNA / TOPOISOMERASE / PROTEIN-DNA COMPLEX / COVALENTLY LINKED COMPLEX / DNA SUPERCOILING / DNA REPLICATION / ATP-binding / DNA-binding / Isomerase / Nucleotide-binding / Nucleus / Phosphoprotein / Isomerase-DNA complex
Function / homology
Function and homology information


replication fork progression beyond termination site / DNA replication termination region / chromatin remodeling at centromere / sister chromatid segregation / regulation of mitotic recombination / resolution of meiotic recombination intermediates / SUMOylation of DNA replication proteins / synaptonemal complex / reciprocal meiotic recombination / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity ...replication fork progression beyond termination site / DNA replication termination region / chromatin remodeling at centromere / sister chromatid segregation / regulation of mitotic recombination / resolution of meiotic recombination intermediates / SUMOylation of DNA replication proteins / synaptonemal complex / reciprocal meiotic recombination / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA strand elongation involved in DNA replication / rRNA transcription / DNA topological change / chromatin organization / mitochondrion / DNA binding / ATP binding / identical protein binding / metal ion binding / nucleus
Similarity search - Function
Dna Ligase; domain 1 - #30 / Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / DNA topoisomerase 2, TOPRIM domain / Rossmann fold - #670 / Gyrase A; domain 2 - #40 / DNA topoisomerase II, eukaryotic-type / C-terminal associated domain of TOPRIM ...Dna Ligase; domain 1 - #30 / Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / DNA topoisomerase 2, TOPRIM domain / Rossmann fold - #670 / Gyrase A; domain 2 - #40 / DNA topoisomerase II, eukaryotic-type / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / 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-like ATPases / 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
3'-THIO-THYMIDINE-5'-PHOSPHATE / DNA / DNA (> 10) / DNA topoisomerase 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsSchmidt, B.H. / Burgin, A.B. / Deweese, J.E. / Osheroff, N. / Berger, J.M.
CitationJournal: Nature / Year: 2010
Title: A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases.
Authors: Schmidt, B.H. / Burgin, A.B. / Deweese, J.E. / Osheroff, N. / Berger, J.M.
History
DepositionDec 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_conn
Revision 1.3Jul 31, 2019Group: Data collection / Derived calculations / Category: chem_comp / struct_conn / Item: _chem_comp.type / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 2
B: DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3')
C: DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)-3')
D: DNA (5'-D(P*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*)-3')
E: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9476
Polymers103,6085
Non-polymers3381
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.045, 92.416, 116.732
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-1120-

ARG

21A-1120-

ARG

31A-181-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA topoisomerase 2 / Topoisomerase / DNA topoisomerase II


Mass: 88025.180 Da / Num. of mol.: 1 / Fragment: RESIDUES 421-1177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: N2244, TOP2, TOR3, YNL088W / Plasmid: PGAL / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): BCY123 / References: UniProt: P06786, EC: 5.99.1.3

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DNA chain , 4 types, 4 molecules BCDE

#2: DNA chain DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3')


Mass: 3269.149 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)-3')


Mass: 4675.035 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: DNA chain DNA (5'-D(P*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*)-3')


Mass: 3109.053 Da / Num. of mol.: 1 / Source method: obtained synthetically
#5: DNA chain DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)-3')


Mass: 4529.949 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 2 types, 114 molecules

#6: Chemical ChemComp-TSP / 3'-THIO-THYMIDINE-5'-PHOSPHATE


Type: DNA linking / Mass: 338.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O7PS
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% 1,4-BUTANEDIOL, 0.1M SODIUM ACETATE, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2009
RadiationMonochromator: DOUBLE FLAT CRYSTAL, SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. all: 33390 / Num. obs: 33390 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 51.9 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 34.5
Reflection shellResolution: 2.48→2.57 Å / Redundancy: 8 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3277 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2RGR

2rgr


Resolution: 2.48→43.022 Å / SU ML: 0.39 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2594 1630 4.89 %RANDOM
Rwork0.2391 ---
obs0.2402 33330 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.484 Å2 / ksol: 0.303 e/Å3
Displacement parametersBiso mean: 77.96 Å2
Baniso -1Baniso -2Baniso -3
1--5.779 Å20 Å20 Å2
2---2.5679 Å20 Å2
3---8.3469 Å2
Refinement stepCycle: LAST / Resolution: 2.48→43.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5941 1039 20 113 7113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097268
X-RAY DIFFRACTIONf_angle_d1.21610022
X-RAY DIFFRACTIONf_dihedral_angle_d19.2822797
X-RAY DIFFRACTIONf_chiral_restr0.0971079
X-RAY DIFFRACTIONf_plane_restr0.0081096
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.48-2.55920.40571280.3212522265097
2.5592-2.64180.37211320.324526172749100
2.6418-2.73620.36711350.309426122747100
2.7362-2.84570.36531320.308426092741100
2.8457-2.97520.39351370.299926282765100
2.9752-3.1320.33431170.301926342751100
3.132-3.32820.30861400.278726202760100
3.3282-3.5850.25521460.259126432789100
3.585-3.94560.21431470.218626082755100
3.9456-4.5160.22261450.181826782823100
4.516-5.68760.18091290.193426962825100
5.6876-43.02890.2121420.201428332975100
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)
10.15450.08370.28570.7977-0.23230.6517-0.3584-0.3824-0.63740.2437-0.1359-0.3910.94150.1256-00.6277-0.03740.26260.41890.11010.726921.945-32.33265.3623
20.3806-0.1750.1780.1023-0.07270.9408-0.52630.1915-0.82960.0949-0.152-0.10850.5697-0.7785-0.00350.4947-0.18460.24840.5823-0.13740.712414.458-29.2392-1.7062
30.16020.1292-0.01980.1160.03670.15060.79180.1991.18320.20250.19950.7348-1.7012-0.05510.00541.5959-0.04030.33271.1217-0.01461.232815.21651.59411.4028
41.0668-0.2762-0.08860.7217-0.73830.8957-0.05820.2316-0.17240.0644-0.2120.4405-0.3443-1.0805-00.3406-0.09470.07790.7065-0.23750.571112.0263-19.4832-8.3922
50.8591-0.1462-0.51011.1725-0.01580.8059-0.13330.0125-0.0875-0.04120.00020.01610.0992-0.0215-0.00010.2067-0.01040.03490.2195-0.0430.188544.8433-14.7667-24.619
60.3343-0.37230.24310.4428-0.29450.1851-0.10220.21730.2341-0.0627-0.27080.3649-0.1234-0.008700.4177-0.0063-0.09580.41740.03060.361635.326219.5797-24.2233
70.3222-0.0865-0.35140.05890.17080.5305-0.4064-0.2520.31520.3229-0.0030.6733-0.3263-0.3101-00.75110.0886-0.29330.4525-0.12770.681630.031537.3389-6.1671
80.0029-0.01170.03010.0705-0.16870.3784-0.1683-0.3639-0.23230.2937-0.2377-0.0009-0.3625-0.08290.00280.6536-0.0812-0.20270.3743-0.03140.48335.208431.1294-4.9761
90.043-0.06330.10510.3419-0.26720.2465-0.13960.0180.11380.28350.0504-0.6001-0.2990.5716-00.6018-0.0564-0.11250.5030.08750.553245.475430.988-21.0912
100.24230.19250.17820.30.17190.11810.07120.0996-0.0846-0.3121-0.0036-0.7056-0.11260.4494-0.00010.3541-0.04380.07490.3715-0.03920.377151.47412.7732-30.4148
110.55-0.00160.0310.1019-0.03510.054-0.5875-0.2115-0.8344-0.29830.0013-0.03730.7926-0.2577-0.02350.8463-0.12820.26150.2327-0.38671.096634.745-28.9253-19.7904
120.5071-0.55560.19411.0199-0.7160.66030.19770.0031-0.7905-0.2067-0.4814-0.12660.28781.91360.04050.326-0.06330.08331.17280.12850.517637.4294-29.2148-17.0105
131.82360.022-0.47570.1768-0.60432.1669-0.29040.2318-1.113-0.2041-0.12360.11431.2642-0.4193-0.01860.4677-0.04820.15220.4976-0.05530.314134.6406-29.1328-19.8773
140.7725-0.42170.68570.3572-0.38160.62250.64150.4139-0.5204-0.4034-0.109-0.1021-0.1080.6178-0.57090.4720.20.26490.3238-0.53990.816637.5191-28.9667-16.7402
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resseq 421:506)A421 - 506
2X-RAY DIFFRACTION2chain A and (resseq 507:563)A507 - 563
3X-RAY DIFFRACTION3chain A and (resseq 564:609)A564 - 609
4X-RAY DIFFRACTION4chain A and (resseq 610:680)A610 - 680
5X-RAY DIFFRACTION5chain A and (resseq 681:988)A681 - 988
6X-RAY DIFFRACTION6chain A and (resseq 989:1035)A989 - 1035
7X-RAY DIFFRACTION7chain A and (resseq 1036:1069)A0
8X-RAY DIFFRACTION8chain A and (resseq 1107:1124)A0
9X-RAY DIFFRACTION9chain A and (resseq 1125:1150)A0
10X-RAY DIFFRACTION10chain A and (resseq 1151:1177)A0
11X-RAY DIFFRACTION11chain BB1 - 11
12X-RAY DIFFRACTION12chain CC1 - 15
13X-RAY DIFFRACTION13chain DD1 - 11
14X-RAY DIFFRACTION14chain EE1 - 15

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