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- EMDB-39077: pP1192R-DNA-m-AMSA complex Overall-2 -

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Entry
Database: EMDB / ID: EMD-39077
TitlepP1192R-DNA-m-AMSA complex Overall-2
Map data
Sample
  • Complex: pP1192R-DNA-m-AMSA complex Overall-2
KeywordsASFV / PROTEIN BINDING
Biological speciesAfrican swine fever virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsSun JQ / liu RL
Funding support China, 1 items
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 6, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39077.png

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Map

FileDownload / File: emd_39077.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
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Contour LevelBy AUTHOR: 0.137
Minimum - Maximum-0.46372396 - 1.6882778
Average (Standard dev.)-0.0013276965 (±0.028231004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39077_half_map_1.map
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Half map: #2

Fileemd_39077_half_map_2.map
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Sample components

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Entire : pP1192R-DNA-m-AMSA complex Overall-2

EntireName: pP1192R-DNA-m-AMSA complex Overall-2
Components
  • Complex: pP1192R-DNA-m-AMSA complex Overall-2

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Supramolecule #1: pP1192R-DNA-m-AMSA complex Overall-2

SupramoleculeName: pP1192R-DNA-m-AMSA complex Overall-2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: African swine fever virus

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.0 mg/mL
BufferpH: 8 / Details: 20mM NaCl,150mM Tris-HCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 170796
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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