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- EMDB-37230: Structure of African swine fever virus topoisomerase II in comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-37230
TitleStructure of African swine fever virus topoisomerase II in complex with dsDNA
Map dataMAP
Sample
  • Complex: pP1192R
    • DNA: DNA (38-MER)
  • DNA: DNA (38-MER)
  • Protein or peptide: DNA topoisomerase 2
Keywordstopo 2 / VIRAL PROTEIN-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
Biological speciesAfrican swine fever virus / DNA molecule (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsCong J / Xin Y / Li X / Chen Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Structural insights into the DNA topoisomerase II of the African swine fever virus.
Authors: Jingyuan Cong / Yuhui Xin / Huiling Kang / Yunge Yang / Chenlong Wang / Dongming Zhao / Xuemei Li / Zihe Rao / Yutao Chen /
Abstract: Type II topoisomerases are ubiquitous enzymes that play a pivotal role in modulating the topological configuration of double-stranded DNA. These topoisomerases are required for DNA metabolism and ...Type II topoisomerases are ubiquitous enzymes that play a pivotal role in modulating the topological configuration of double-stranded DNA. These topoisomerases are required for DNA metabolism and have been extensively studied in both prokaryotic and eukaryotic organisms. However, our understanding of virus-encoded type II topoisomerases remains limited. One intriguing example is the African swine fever virus, which stands as the sole mammalian-infecting virus encoding a type II topoisomerase. In this work, we use several approaches including cryo-EM, X-ray crystallography, and biochemical assays to investigate the structure and function of the African swine fever virus type II topoisomerase, pP1192R. We determine the structures of pP1192R in different conformational states and confirm its enzymatic activity in vitro. Collectively, our results illustrate the basic mechanisms of viral type II topoisomerases, increasing our understanding of these enzymes and presenting a potential avenue for intervention strategies to mitigate the impact of the African swine fever virus.
History
DepositionAug 19, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37230.png

Downloads & links

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Map

FileDownload / File: emd_37230.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMAP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 295.2 Å		0.82 Å/pix.
x 360 pix.
= 295.2 Å		0.82 Å/pix.
x 360 pix.
= 295.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.0067689978 - 0.017664375
Average (Standard dev.)0.00012758479 (±0.0007954781)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 295.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: HALFMAP

Fileemd_37230_half_map_1.map
AnnotationHALFMAP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HALFMAP

Fileemd_37230_half_map_2.map
AnnotationHALFMAP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : pP1192R

EntireName: pP1192R
Components
  • Complex: pP1192R
    • DNA: DNA (38-MER)
  • DNA: DNA (38-MER)
  • Protein or peptide: DNA topoisomerase 2

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Supramolecule #1: pP1192R

SupramoleculeName: pP1192R / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: dimer
Source (natural)Organism: African swine fever virus

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Macromolecule #1: DNA (38-MER)

MacromoleculeName: DNA (38-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 16.058391 KDa
SequenceString: (DA)(DT)(DG)(DC)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DG)(DT) (DA)(DT)(DG)(DT)(DG)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA)(DC)(DA) (DT) (DA)(DT)(DA)(DT)(DA)(DT) ...String:
(DA)(DT)(DG)(DC)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DG)(DT) (DA)(DT)(DG)(DT)(DG)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA)(DC)(DA) (DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)

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Macromolecule #2: DNA (38-MER)

MacromoleculeName: DNA (38-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 15.965361 KDa
SequenceString: (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DG)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC)(DA)(DC)(DA) (DC)(DA)(DT)(DA)(DC)(DA)(DT)(DA)(DT)(DA) (DC) (DA)(DT)(DA)(DT)(DA)(DT) ...String:
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DG)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC)(DA)(DC)(DA) (DC)(DA)(DT)(DA)(DC)(DA)(DT)(DA)(DT)(DA) (DC) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DG)(DC)(DA)(DT)

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Macromolecule #3: DNA topoisomerase 2

MacromoleculeName: DNA topoisomerase 2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 138.093359 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: EFATMEAFEI SDFKEHAKKK SMWAGALNKV TISGLMGVFT EDEDLMALPI HRDHCPALLK IFDEIIVNAT DHERACHNKT KKVTYIKIS FDKGVFSCEN DGPGIPIAKH EQASLIAKRD VYVPEVASCH FLAGTNINKA KDCIKGGTNG VGLKLAMVHS Q WAILTTAD ...String:
EFATMEAFEI SDFKEHAKKK SMWAGALNKV TISGLMGVFT EDEDLMALPI HRDHCPALLK IFDEIIVNAT DHERACHNKT KKVTYIKIS FDKGVFSCEN DGPGIPIAKH EQASLIAKRD VYVPEVASCH FLAGTNINKA KDCIKGGTNG VGLKLAMVHS Q WAILTTAD GAQKYVQHIN QRLDIIEPPT ITPSREMFTR IELMPVYQEL GYAEPLSETE QADLSAWIYL RACQCAAYVG KG TTIYYND KPCRTGSVMA LAKMYTLLSA PNSTIHTATI KADAKPYSLH PLQVAAVVSP KFKKFEHVSV INGVNCVKGE HVT FLKKTI NEMVVKKFQQ TIKDKNRKTT LRDSCSNIFI VIVGSIPGIE WTGQRKDELS IAENVFKTHY SIPSSFLTSM TKSI VDILL QSISKKDNHK QVDVDKYTRA RNAGGKRAQD CMLLAAEGDS ALSLLRTGLT LGKSNPSGPS FDFCGMISLG GVIMN ACKK VTNITTDSGE TIMVRNEQLT NNKVLQGIVQ VLGLDFNCHY KTQEERAKLR YGCIVACVDQ DLDGCGKILG LLLAYF HLF WPQLIIHGFV KRLLTPLIRV YEKGKTMPVE FYYEQEFDAW AKKQTSLANH TVKYYKGLAA HDTHEVKSMF KHFDNMV YT FTLDDSAKEL FHIYFGGESE LRKRELCTGV VPLTETQTQS IHSVRRIPCS LHLQVDTKAY KLDAIERQIP NFLDGMTR A RRKILAGGVK CFASNNRERK VFQFGGYVAD HMFYHHGDMS LNTSIIKAAQ YYPGSSHLYP VFIGIGSFGS RHLGGKDAG SPRYISVQLA SEFIKTMFPA EDSWLLPYVF EDGQRAEPEY YVPVLPLAIM EYGANPSEGW KYTTWARQLE DILALVRAYV DKDNPKHEL LHYAIKHKIT ILPLRPSNYN FKGHLKRFGQ YYYSYGTYVI SEQRNIITIT ELPLRVPTVA YIESIKKSSN R MTFIEEII DYSSSETIEI LVKLKPNSLN RIVEEFKETE EQDSIENFLR LRNCLHSHLN FVKPKGGIIE FNTYYEILYA WL PYRRELY QKRLMREHAV LKLRIIMETA IVRYINESAE LNLSHYEDEK EASRILSEHG FPPLNHTLII SPEFASIEEL NQK ALQGCY TYILSLQARE LLIAAKTRRV EKIKKMQARL DKVEQLLQES PFPGASVWLE EIDAVEKAII KGRNTQWKFH ENLY FQGHH HHHHHH

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

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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