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- PDB-3l4k: Topoisomerase II-DNA cleavage complex, metal-bound -

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Basic information

Entry
Database: PDB / ID: 3l4k
TitleTopoisomerase II-DNA cleavage complex, metal-bound
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 2
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 / regulation of mitotic recombination / sister chromatid segregation / 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 / regulation of mitotic recombination / sister chromatid segregation / 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 / DNA topological change / rRNA transcription / chromatin organization / mitochondrion / DNA binding / ATP binding / identical protein binding / nucleus / metal ion binding
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: 2.98 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 / pdbx_struct_conn_angle / struct_conn / 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_alt_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_alt_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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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)104,47014
Polymers103,6085
Non-polymers8629
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.064, 91.851, 115.939
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-116-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA topoisomerase 2 / 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 , 3 types, 29 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.2 Å3/Da / Density % sol: 44.21 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% 1,4-BUTANEDIOL, 0.1M SODIUM ACETATE, pH 6.5, 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: 1.2823 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2009
RadiationMonochromator: DOUBLE FLAT CRYSTAL, SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2823 Å / Relative weight: 1
ReflectionResolution: 2.98→50 Å / Num. all: 19750 / Num. obs: 18071 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 72.6 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.6
Reflection shellResolution: 2.98→3.07 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1827 / % possible all: 94

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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: 2.98→49.023 Å / SU ML: 0.42 / σ(F): 1.9 / Stereochemistry target values: ML / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflectionSelection details
Rfree0.2733 1549 4.97 %IMPORTED FROM PDB ENTRY 3L4J
Rwork0.2391 ---
obs0.2408 17619 86.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.228 Å2 / ksol: 0.266 e/Å3
Displacement parametersBiso mean: 89.9 Å2
Baniso -1Baniso -2Baniso -3
1--8.8659 Å20 Å20 Å2
2--14.0089 Å20 Å2
3----5.143 Å2
Refinement stepCycle: LAST / Resolution: 2.98→49.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5941 1039 28 20 7028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087257
X-RAY DIFFRACTIONf_angle_d1.2510013
X-RAY DIFFRACTIONf_dihedral_angle_d18.0722802
X-RAY DIFFRACTIONf_chiral_restr0.1031079
X-RAY DIFFRACTIONf_plane_restr0.0071096
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.98-3.07950.39431270.33732722284986
3.0795-3.18950.3651290.33012740286988
3.1895-3.31720.3981530.32762710286388
3.3172-3.46820.32611710.2992705287687
3.4682-3.6510.3471430.27252706284987
3.651-3.87960.29041570.25492716287387
3.8796-4.1790.28261370.22912687282486
4.179-4.59930.24571390.19712660279985
4.5993-5.26410.18751320.19612659279185
5.2641-6.62970.26771130.2132683279685
6.6297-49.02920.2091480.19352643279185

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