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- PDB-8ygg: pP1192R-apo Closed state -

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Basic information

Entry
Database: PDB / ID: 8ygg
TitlepP1192R-apo Closed state
ComponentsDNA topoisomerase 2
KeywordsISOMERASE / ASFV / PROTEIN BINDING
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
Biological speciesAfrican swine fever virus pig/Kenya/KEN-50/1950
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 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
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA topoisomerase 2
B: DNA topoisomerase 2


Theoretical massNumber of molelcules
Total (without water)271,7202
Polymers271,7202
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 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 / Production host: Homo sapiens (human)
References: UniProt: A0A0C5B080, DNA topoisomerase (ATP-hydrolysing)
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: pP1192R-apo Closed state / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78195 / Symmetry type: POINT

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