+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36119 | |||||||||
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Title | Cryo-EM structure of viral topoisomerase in conformation 1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | topoisomerase / VIRAL PROTEIN | |||||||||
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 / host cell cytoplasm / DNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | African swine fever virus LIS57 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.16 Å | |||||||||
Authors | Deng Z | |||||||||
Funding support | 1 items
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Citation | Journal: mBio / Year: 2023 Title: Cryo-EM structures of African swine fever virus topoisomerase. Authors: Yan Zhao / Wenhua Kuang / Qiyin An / Jinyue Li / Yong Wang / Zengqin Deng / Abstract: African swine fever virus (ASFV) is a highly contagious virus that causes lethal hemorrhagic diseases known as African swine fever (ASF) with a case fatality rate of 100%. There is an urgent need to ...African swine fever virus (ASFV) is a highly contagious virus that causes lethal hemorrhagic diseases known as African swine fever (ASF) with a case fatality rate of 100%. There is an urgent need to develop anti-ASFV drugs. We determine the first high-resolution structures of viral topoisomerase ASFV P1192R in both the closed and open C-gate forms. P1192R shows a similar overall architecture with eukaryotic and prokaryotic type II topoisomerases, which have been successful targets of many antimicrobials and anticancer drugs, with the most similarity to yeast topo II. P1192R also exhibits differences in the details of active site configuration, which are important to enzyme activity. These two structures offer useful structural information for antiviral drug design and provide structural evidence to support that eukaryotic type IIA topoisomerase likely originated from horizontal gene transfer from the virus. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36119.map.gz | 97.2 MB | EMDB map data format | |
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Header (meta data) | emd-36119-v30.xml emd-36119.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
Images | emd_36119.png | 12.6 KB | ||
Filedesc metadata | emd-36119.cif.gz | 5.7 KB | ||
Others | emd_36119_half_map_1.map.gz emd_36119_half_map_2.map.gz | 95.4 MB 95.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36119 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36119 | HTTPS FTP |
-Validation report
Summary document | emd_36119_validation.pdf.gz | 878.1 KB | Display | EMDB validaton report |
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Full document | emd_36119_full_validation.pdf.gz | 877.6 KB | Display | |
Data in XML | emd_36119_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | emd_36119_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36119 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36119 | HTTPS FTP |
-Related structure data
Related structure data | 8j9yMC 8j9zC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_36119.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.95 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_36119_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36119_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : P1192R
Entire | Name: P1192R |
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Components |
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-Supramolecule #1: P1192R
Supramolecule | Name: P1192R / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: African swine fever virus LIS57 |
Molecular weight | Theoretical: 135 kDa/nm |
-Macromolecule #1: DNA topoisomerase 2
Macromolecule | Name: DNA topoisomerase 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: African swine fever virus LIS57 |
Molecular weight | Theoretical: 135.687859 KDa |
Recombinant expression | Organism: Komagataella pastoris (fungus) |
Sequence | String: MEAFEISDFK EHAKKKSMWA GALNKVTISG LMGVFTEDED LMALPIHRDH CPALLKIFDE IIVNATDHER ACHNKTKKVT YIKISFDKG VFSCENDGPG IPIAKHEQAS LIAKRDVYVP EVASCHFLAG TNINKAKDCI KGGTNGVGLK LAMVHSQWAI L TTADGAQK ...String: MEAFEISDFK EHAKKKSMWA GALNKVTISG LMGVFTEDED LMALPIHRDH CPALLKIFDE IIVNATDHER ACHNKTKKVT YIKISFDKG VFSCENDGPG IPIAKHEQAS LIAKRDVYVP EVASCHFLAG TNINKAKDCI KGGTNGVGLK LAMVHSQWAI L TTADGAQK YVQHINQRLD IIEPPTITPS REMFTRIELM PVYQELGYAE PLSETEQADL SAWIYLRACQ CAAYVGKGTT IY YNDKPCR TGSVMALAKM YTLLSAPNST IHTATIKADA KPYSLHPLQV AAVVSPKFKK FEHVSVINGV NCVKGEHVTF LKK TINEMV VKKFQQTIKD KNRKTTLRDS CSNIFIVIVG SIPGIEWTGQ RKDELSIAEN VFKTHYSIPS SFLTSMTKSI VDIL LQSIS KKDNHKQVDV DKYTRARNAG GKRAQDCMLL AAEGDSALSL LRTGLTLGKS NPSGPSFDFC GMISLGGVIM NACKK VTNI TTDSGETIMV RNEQLTNNKV LQGIVQVLGL DFNCHYKTQE ERAKLRYGCI VACVDQDLDG CGKILGLLLA YFHLFW PQL IIHGFVKRLL TPLIRVYEKG KTMPVEFYYE QEFDAWAKKQ TSLANHTVKY YKGLAAHDTH EVKSMFKHFD NMVYTFT LD DSAKELFHIY FGGESELRKR ELCTGVVPLT ETQTQSIHSV RRIPCSLHLQ VDTKAYKLDA IERQIPNFLD GMTRARRK I LAGGVKCFAS NNRERKVFQF GGYVADHMFY HHGDMSLNTS IIKAAQYYPG SSHLYPVFIG IGSFGSRHLG GKDAGSPRY ISVQLASEFI KTMFPAEDSW LLPYVFEDGQ RAEPEYYVPV LPLAIMEYGA NPSEGWKYTT WARQLEDILA LVRAYVDKDN PKHELLHYA IKHKITILPL RPSNYNFKGH LKRFGQYYYS YGTYVISEQR NIITITELPL RVPTVAYIES IKKSSNRMTF I EEIIDYSS SETIEILVKL KPNSLNRIVE EFKETEEQDS IENFLRLRNC LHSHLNFVKP KGGIIEFNTY YEILYAWLPY RR ELYQKRL MREHAVLKLR IIMETAIVRY INESAELNLS HYEDEKEASR ILSEHGFPPL NHTLIISPEF ASIEELNQKA LQG CYTYIL SLQARELLIA AKTRRVEKIK KMQARLDKVE QLLQESPFPG ASVWLEEIDA VEKAIIKGRN TQWKFH UniProtKB: DNA topoisomerase 2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 135059 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |