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- PDB-8yge: pP1192R-DNA-m-AMSA complex DNA binding/cleavage domain -

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Basic information

Entry
Database: PDB / ID: 8yge
TitlepP1192R-DNA-m-AMSA complex DNA binding/cleavage domain
Components
  • DNA (12-mer)
  • DNA (20-mer)
  • DNA (8-mer)
  • DNA topoisomerase 2
KeywordsISOMERASE/DNA / ASFV / PROTEIN BINDING / ISOMERASE-DNA complex
Function / homology
Function and homology information


sister chromatid segregation / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / DNA topoisomerase II, eukaryotic-type / : / 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 ...C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / DNA topoisomerase II, eukaryotic-type / : / 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 / 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/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 2
Similarity search - Component
Biological speciesAfrican swine fever virus pig/Kenya/KEN-50/1950
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsSun, J.Q. / Liu, R.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270157 China
CitationJournal: Nucleic Acids Res / Year: 2024
Title: Structural basis for difunctional mechanism of m-AMSA against African swine fever virus pP1192R.
Authors: Ruili Liu / Junqing Sun / Lian-Feng Li / Yingxian Cheng / Meilin Li / Lifeng Fu / Su Li / Guorui Peng / Yanjin Wang / Sheng Liu / Xiao Qu / Jiaqi Ran / Xiaomei Li / Erqi Pang / Hua-Ji Qiu / ...Authors: Ruili Liu / Junqing Sun / Lian-Feng Li / Yingxian Cheng / Meilin Li / Lifeng Fu / Su Li / Guorui Peng / Yanjin Wang / Sheng Liu / Xiao Qu / Jiaqi Ran / Xiaomei Li / Erqi Pang / Hua-Ji Qiu / Yanli Wang / Jianxun Qi / Han Wang / George Fu Gao /
Abstract: The African swine fever virus (ASFV) type II topoisomerase (Topo II), pP1192R, is the only known Topo II expressed by mammalian viruses and is essential for ASFV replication in the host cytoplasm. ...The African swine fever virus (ASFV) type II topoisomerase (Topo II), pP1192R, is the only known Topo II expressed by mammalian viruses and is essential for ASFV replication in the host cytoplasm. Herein, we report the structures of pP1192R in various enzymatic stages using both X-ray crystallography and single-particle cryo-electron microscopy. Our data structurally define the pP1192R-modulated DNA topology changes. By presenting the A2+-like metal ion at the pre-cleavage site, the pP1192R-DNA-m-AMSA complex structure provides support for the classical two-metal mechanism in Topo II-mediated DNA cleavage and a better explanation for nucleophile formation. The unique inhibitor selectivity of pP1192R and the difunctional mechanism of pP1192R inhibition by m-AMSA highlight the specificity of viral Topo II in the poison binding site. Altogether, this study provides the information applicable to the development of a pP1192R-targeting anti-ASFV strategy.
History
DepositionFeb 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 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 2
B: DNA topoisomerase 2
C: DNA (20-mer)
D: DNA (8-mer)
E: DNA (12-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,80210
Polymers283,9425
Non-polymers8605
Water00
1


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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA topoisomerase 2 / DNA topoisomerase II


Mass: 135859.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus pig/Kenya/KEN-50/1950
Gene: BA71V-P1192R (i7R), P1192R / Cell (production host): 293f / Production host: Homo sapiens (human)
References: UniProt: A0A0C5B080, DNA topoisomerase (ATP-hydrolysing)

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DNA chain , 3 types, 3 molecules CDE

#2: DNA chain DNA (20-mer)


Mass: 6189.014 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) African swine fever virus pig/Kenya/KEN-50/1950
#3: DNA chain DNA (8-mer)


Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) African swine fever virus pig/Kenya/KEN-50/1950
#4: DNA chain DNA (12-mer)


Mass: 3606.381 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) African swine fever virus pig/Kenya/KEN-50/1950

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Non-polymers , 2 types, 5 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#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 / Comment: antineoplastic*YM

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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: pP1192R-DNA-m-AMSA complex DNA binding/cleavage domain
Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Source (natural)Organism: African swine fever virus pig/Kenya/KEN-50/1950
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8 / Details: 20mM NaCl,150mM Tris-HCl
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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: 1000 nm / Cs: 0.001 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 271076 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00413873
ELECTRON MICROSCOPYf_angle_d0.5818920
ELECTRON MICROSCOPYf_dihedral_angle_d15.2252127
ELECTRON MICROSCOPYf_chiral_restr0.042050
ELECTRON MICROSCOPYf_plane_restr0.0032272

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