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- PDB-9jnk: Bacteriophage T4 topoisomerse II bound with a T-segment DNA -

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Basic information

Entry
Database: PDB / ID: 9jnk
TitleBacteriophage T4 topoisomerse II bound with a T-segment DNA
Components
  • (DNA (25-MER)) x 2
  • DNA topoisomerase large subunit,DNA topoisomerase small subunit
  • DNA topoisomerase medium subunit
KeywordsISOMERASE/DNA / Type IIA topoisomerase / T-segment DNA / ISOMERASE-DNA complex
Function / homology
Function and homology information


sister chromatid segregation / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / protein-containing complex / DNA binding / ATP binding
Similarity search - Function
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 ...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 / DNA topoisomerase, type IIA-like domain superfamily / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA topoisomerase medium subunit / DNA topoisomerase large subunit / DNA topoisomerase small subunit
Similarity search - Component
Biological speciesEscherichia phage T4 (virus)
DNA molecule (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsXin, Y.H. / Chen, Y.T.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Sci Adv / Year: 2025
Title: Direct trapping of the transport-segment DNA by the central domain of type IIA topoisomerases.
Authors: Yuhui Xin / Runqi Xian / Congrong Liu / Oujia Zhang / Zihe Rao / Xuemei Li / Yutao Chen /
Abstract: Type IIA topoisomerases modulate DNA topology by coordinating the cleavage of gate-segment DNA and the passage of transport-segment DNA-a mechanism conserved across species and essential for diverse ...Type IIA topoisomerases modulate DNA topology by coordinating the cleavage of gate-segment DNA and the passage of transport-segment DNA-a mechanism conserved across species and essential for diverse cellular processes. While gate-segment interactions have been extensively studied, direct structural evidence of transport-segment capture has remained elusive, limiting our understanding of the full catalytic cycle. Here, we present a cryo-electron microscopy structure of the T4 bacteriophage topoisomerase II with a transport-segment DNA bound directly to its central domain. The structure reveals conformational rearrangements in the central domain that accommodate the transport-segment DNA, suggesting an alternative sequence of events in which the enzyme sliding along the loosely bound religated gate segment may precede transport-segment passage through the coiled-coil gate. Supported by mutational and biochemical assays, our findings provide previously unidentified mechanistic insights and open potential avenues for the development of next-generation type IIA topoisomerase inhibitors.
History
DepositionSep 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase large subunit,DNA topoisomerase small subunit
C: DNA topoisomerase medium subunit
B: DNA topoisomerase large subunit,DNA topoisomerase small subunit
D: DNA topoisomerase medium subunit
E: DNA (25-MER)
F: DNA (25-MER)


Theoretical massNumber of molelcules
Total (without water)274,2986
Polymers274,2986
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein DNA topoisomerase large subunit,DNA topoisomerase small subunit / DNA topoisomerase 64-kDa subunit / Protein Gp39 / DNA topoisomerase 18-kDa subunit / Protein Gp60


Mass: 77524.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: fusion protein (gp39+gp60) / Source: (gene. exp.) Escherichia phage T4 (virus) / Gene: 39, 60 / Production host: Escherichia coli (E. coli)
References: UniProt: P09176, UniProt: P23992, DNA topoisomerase (ATP-hydrolysing)
#2: Protein DNA topoisomerase medium subunit / DNA topoisomerase 51-kDa subunit / Protein Gp52


Mass: 51951.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage T4 (virus) / Gene: 52 / Production host: Escherichia coli (E. coli)
References: UniProt: P07065, DNA topoisomerase (ATP-hydrolysing)
#3: DNA chain DNA (25-MER)


Mass: 7668.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#4: DNA chain DNA (25-MER)


Mass: 7677.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bacteriophage T4 topoisomerase II central domian bound with a T-segment DNA
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Enterobacteria phage T4 (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 164653 / Symmetry type: POINT

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