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- PDB-8yo7: structure of phage T6 topoisomerase II central domain bound with ... -

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Basic information

Entry
Database: PDB / ID: 8yo7
Titlestructure of phage T6 topoisomerase II central domain bound with DNA and m-AMSA
Components
  • (DNA topoisomerase ...) x 2
  • DNA (5'-D(P*AP*TP*AP*TP*AP*CP*AP*CP*AP*TP*AP*T)-3')
  • DNA (5'-D(P*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*A)-3')
KeywordsISOMERASE / topoisomerase II
Function / homology
Function and homology information


sister chromatid segregation / DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / protein-containing complex / DNA binding / ATP binding
Similarity search - Function
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 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
Chem-ASW / DNA / DNA (> 10) / DNA topoisomerase (ATP-hydrolyzing) / DNA topoisomerase medium subunit
Similarity search - Component
Biological speciesEscherichia phage T4 (virus)
Enterobacteria phage T6 (virus)
DNA molecule (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsChen, Y.T. / Xin, Y.H. / Xian, R.Q.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To be published
Title: structure of phage T6 topoisomerase II central domain bound with DNA and m-AMSA
Authors: Chen, Y.T. / Xin, Y.H. / Xian, R.Q.
History
DepositionMar 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2024Provider: 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 medium subunit
B: DNA topoisomerase medium subunit
C: DNA topoisomerase (ATP-hydrolyzing)
D: DNA topoisomerase (ATP-hydrolyzing)
E: DNA (5'-D(P*AP*TP*AP*TP*AP*CP*AP*CP*AP*TP*AP*T)-3')
F: DNA (5'-D(P*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*A)-3')
X: DNA (5'-D(P*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*A)-3')
Y: DNA (5'-D(P*AP*TP*AP*TP*AP*CP*AP*CP*AP*TP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,26212
Polymers306,4268
Non-polymers8364
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA topoisomerase ... , 2 types, 4 molecules ABCD

#1: 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)
#2: Protein DNA topoisomerase (ATP-hydrolyzing) / phage T6 topoisomerase II gp39 subunit


Mass: 69237.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T6 (virus) / Gene: EcT6_00003 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A346FJ89, DNA topoisomerase (ATP-hydrolysing)

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DNA chain , 2 types, 4 molecules EYFX

#3: DNA chain DNA (5'-D(P*AP*TP*AP*TP*AP*CP*AP*CP*AP*TP*AP*T)-3')


Mass: 16058.391 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#4: DNA chain DNA (5'-D(P*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*A)-3')


Mass: 15965.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)

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Non-polymers , 3 types, 6 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ASW / N-[4-(acridin-9-ylamino)-3-methoxyphenyl]methanesulfonamide / Amsacrine


Mass: 393.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H19N3O3S / Feature type: SUBJECT OF INVESTIGATION / Comment: antineoplastic*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: Phage T6 topoisomerase II central domain bound with DNA and m-AMSA
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Enterobacteria phage T6 (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: 2500 nm / Nominal defocus min: 1500 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: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 459464 / Symmetry type: POINT

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