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Yorodumi- EMDB-37228: Structure of African swine fever virus topoisomerase II in comple... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37228 | |||||||||
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Title | Structure of African swine fever virus topoisomerase II in complex with dsDNA | |||||||||
Map data | map | |||||||||
Sample |
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Keywords | topo 2 / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information 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 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Jingyuan C / Yuhui X / Xuemei L / Chen Y | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: Structure of African swine fever virus topoisomerase II in complex with dsDNA Authors: Jingyuan C / Yuhui X / Xuemei L / Chen Y | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37228.map.gz | 96.5 MB | EMDB map data format | |
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Header (meta data) | emd-37228-v30.xml emd-37228.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37228_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_37228.png | 59.9 KB | ||
Filedesc metadata | emd-37228.cif.gz | 5.7 KB | ||
Others | emd_37228_half_map_1.map.gz emd_37228_half_map_2.map.gz | 79.5 MB 79.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37228 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37228 | HTTPS FTP |
-Related structure data
Related structure data | 8kgoMC 8kglC 8kgmC 8kgnC 8kgpC 8kgqC 8kgrC 8kgsC 8kgtC 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_37228.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.65 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: map
File | emd_37228_half_map_1.map | ||||||||||||
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Annotation | map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap
File | emd_37228_half_map_2.map | ||||||||||||
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Annotation | halfmap | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : pP1192R
Entire | Name: pP1192R |
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Components |
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-Supramolecule #1: pP1192R
Supramolecule | Name: pP1192R / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: dimer |
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Source (natural) | Organism: African swine fever virus |
-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 |
Molecular weight | Theoretical: 138.093359 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |