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- EMDB-39250: pP1192R-apo open state -

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Basic information

Entry
Database: EMDB / ID: EMD-39250
TitlepP1192R-apo open state
Map data
Sample
  • Complex: pP1192R-apo open state
    • Protein or peptide: DNA topoisomerase 2
KeywordsASFV / PROTEIN BINDING / ISOMERASE
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
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 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 26, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39250.png

Downloads & links

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Map

FileDownload / File: emd_39250.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.272
Minimum - Maximum-0.44744805 - 1.4035934
Average (Standard dev.)-0.00018963142 (±0.041340448)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39250_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_39250_half_map_2.map
Projections & Slices
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Sample components

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Entire : pP1192R-apo open state

EntireName: pP1192R-apo open state
Components
  • Complex: pP1192R-apo open state
    • Protein or peptide: DNA topoisomerase 2

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Supramolecule #1: pP1192R-apo open state

SupramoleculeName: pP1192R-apo open state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: African swine fever virus pig/Kenya/KEN-50/1950

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Macromolecule #1: DNA topoisomerase 2

MacromoleculeName: DNA topoisomerase 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA topoisomerase (ATP-hydrolysing)
Source (natural)Organism: African swine fever virus pig/Kenya/KEN-50/1950
Molecular weightTheoretical: 135.583609 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METFEISDFK EHAKKKSMWA GALNKVTISG LMGVFTEDED LMALPIHRDH CPALLKIFDE LIVNATDHER ACHNKTKKVT YIKISFDKG VFSCENDGPG IPIVKHEQAS LIAKRDVYVP EVASCYFLAG TNINKAKDCI KGGTNGVGLK LAMVHSQWAI L TTADGSQK ...String:
METFEISDFK EHAKKKSMWA GALNKVTISG LMGVFTEDED LMALPIHRDH CPALLKIFDE LIVNATDHER ACHNKTKKVT YIKISFDKG VFSCENDGPG IPIVKHEQAS LIAKRDVYVP EVASCYFLAG TNINKAKDCI KGGTNGVGLK LAMVHSQWAI L TTADGSQK YVQHINQRLD NIEPPTITPS REMFTRIELM PVYQELGYAQ PLSETEQADL SAWIYLRACQ CAAYVGKGTT IY YNDKPCS TSSVMALAKM YTLVTAPNST IYTATIKADA KPYSLHPLQV AAVVSPKFKK FEHVSIINGV NCVKGEHVTF LKK AINEMV VKKFQQTIKD KNRKTTLRDS CSNIFVVIVG SIPGIEWTGQ RKDELSIAEN VFKTHYSIPS SFLTSMTRSI VDIL LQSIS KKDNHKQIDV DKYTRARNAG GKKAQDCMLL AAEGDSALSL LRAGLTLGKS NPSGPSFDFC GMISLGGVIM NACKK VTNI TTDSGETIMV RNEQLTNNKV LQGIVQVLGL DFNCHYKTQE ERAKLRYGCI VACVDQDLDG CGKILGLLLA YFHLFW PQL IVHGFVKRLL TPLIRVYEKG NTVPVEFYYE QEFDAWAKKQ TSLANHTVKY YKGLAAHDTH EVKSMFKHFD KMVYTFT LD DSAKELFHIY FGGESELRKR ELCTGVVPLT ETQTQSIHSV RRIPCSLHLQ VDTKAYKLDA IERQIPNFLD GMTRARRK I LAGGLKCFAS NNRERKVFQF GGYVADHMFY HHGDMSLNTS IIKAAQYYPG SSHLYPVFIG IGSFGSRHLG GKDAGSPRY ISVQLASEFI KTMFPTEDSW LLPYVFEDGQ RAEPEYYVPV LPLAIMEYGA NPSEGWKYTT WARQLEDILA LVRAYVDKNN PKHELLHYA IDHKITVLPL RPSNYNFKGH LKRFGQYYYS YGTYVVSEQR NMITITELPL RVPTVAYIES IKKSSNRMAF I EEIVDYSS SETIEILVKL KPNSLSRIME EFKETEEQNS IENFLRLRNC LHSHLNFVKP KGGIIEFNSY YEILYAWLPY RR DLYQKRL MRERAVLKLR LIMETAIVRY INESADLNLS HYEDEKEAGR ILSEHGFPPL NQSLITSPEF ATIEELNQKA LQG CYTYIL SLQARELLIA AKTRRVEKIK KMQARLDKVE QLLQESPFPG ASVWLEEIDA VEKAIIKGRN TQWKFH

UniProtKB: DNA topoisomerase 2

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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: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131161
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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