+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-45376 | |||||||||
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Title | Human TOP3B-TDRD3 core complex in DNA pre-cleavage state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Topoisomerase / DNA / ISOMERASE-DNA complex | |||||||||
Function / homology | Function and homology information DNA topoisomerase III-beta-TDRD3 complex / DNA topoisomerase activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / condensed chromosome / methylated histone binding / chromosome segregation / chromatin organization / DNA recombination ...DNA topoisomerase III-beta-TDRD3 complex / DNA topoisomerase activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / condensed chromosome / methylated histone binding / chromosome segregation / chromatin organization / DNA recombination / transcription coactivator activity / DNA repair / chromatin binding / Golgi apparatus / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.35 Å | |||||||||
Authors | Yang X / Chen X / Yang W / Pommier Y | |||||||||
Funding support | United States, 2 items
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Citation | Journal: To Be Published Title: Structural Insights into human Topoisomerase 3-beta DNA and RNA catalytic cycles and topo-gate dynamics Authors: Yang X / Chen X / Yang W / Pommier Y | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_45376.map.gz | 143.7 MB | EMDB map data format | |
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Header (meta data) | emd-45376-v30.xml emd-45376.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
Images | emd_45376.png | 41.4 KB | ||
Filedesc metadata | emd-45376.cif.gz | 5.9 KB | ||
Others | emd_45376_half_map_1.map.gz emd_45376_half_map_2.map.gz | 154.2 MB 154.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-45376 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-45376 | HTTPS FTP |
-Validation report
Summary document | emd_45376_validation.pdf.gz | 889.8 KB | Display | EMDB validaton report |
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Full document | emd_45376_full_validation.pdf.gz | 889.4 KB | Display | |
Data in XML | emd_45376_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | emd_45376_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45376 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45376 | HTTPS FTP |
-Related structure data
Related structure data | 9c9yMC 9ca0C 9ca1C 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_45376.map.gz / Format: CCP4 / Size: 166.4 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: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_45376_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_45376_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human TOP3B-TDRD3 core complex with DNA
Entire | Name: human TOP3B-TDRD3 core complex with DNA |
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Components |
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-Supramolecule #1: human TOP3B-TDRD3 core complex with DNA
Supramolecule | Name: human TOP3B-TDRD3 core complex with DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: DNA topoisomerase 3-beta-1
Macromolecule | Name: DNA topoisomerase 3-beta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA topoisomerase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 69.021875 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: VMKTVLMVAE KPSLAQSIAK ILSRGSLSSH KGLNGACSVH EYTGTFAGQP VRFKMTSVCG HVMTLDFLGK YNKWDKVDPA ELFSQAPTE KKEANPKLNM VKFLQVEGRG CDYIVLWLDC DKEGENICFE VLDAVLPVMN KAHGGEKTVF RARFSSITDT D ICNAMACL ...String: VMKTVLMVAE KPSLAQSIAK ILSRGSLSSH KGLNGACSVH EYTGTFAGQP VRFKMTSVCG HVMTLDFLGK YNKWDKVDPA ELFSQAPTE KKEANPKLNM VKFLQVEGRG CDYIVLWLDC DKEGENICFE VLDAVLPVMN KAHGGEKTVF RARFSSITDT D ICNAMACL GEPDHNEALS VDARQELDLR IGCAFTRFQT KYFQGKYGDL DSSLISFGPC QTPTLGFCVE RHDKIQSFKP ET YWVLQAK VNTDKDRSLL LDWDRVRVFD REIAQMFLNM TKLEKEAQVE ATSRKEKAKQ RPLALNTVEM LRVASSSLGM GPQ HAMQTA ERLYTQGYIS FPRTETTHYP ENFDLKGSLR QQANHPYWAD TVKRLLAEGI NRPRKGHDAG DHPPITPMKS ATEA ELGGD AWRLYEYITR HFIATVSHDC KYLQSTISFR IGPELFTCSG KTVLSPGFTE VMPWQSVPLE ESLPTCQRGD AFPVG EVKM LEKQTNPPDY LTEAELITLM EKHGIGTDAS IPVHINNICQ RNYVTVESGR RLKPTNLGIV LVHGYYKIDA ELVLPT IRS AVEKQLNLIA QGKADYRQVL GHTLDVFKRK FHYFVDSIAG MDELMEVSF UniProtKB: DNA topoisomerase 3-beta-1 |
-Macromolecule #2: Tudor domain-containing protein 3
Macromolecule | Name: Tudor domain-containing protein 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 17.428951 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAQVAGAALS QAGWYLSDEG IEACTSSPDK VNVNDIILIA LNTDLRTIGK KFLPSDINSG KVEKLEGPCV LQIQKIRNVA APKDNEESQ AAPRMLRLQM TDGHISCTAV EFSYMSKISL NTPPGTKVKL SGIVDIKNGF LLLNDSNTTV LGGEVEHLIE K W UniProtKB: Tudor domain-containing protein 3 |
-Macromolecule #3: DNA (5'-D(P*AP*CP*TP*AP*AP*AP*AP*T)-3')
Macromolecule | Name: DNA (5'-D(P*AP*CP*TP*AP*AP*AP*AP*T)-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 2.418644 KDa |
Sequence | String: (DA)(DC)(DT)(DA)(DA)(DA)(DA)(DT) |
-Macromolecule #4: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MN |
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Molecular weight | Theoretical: 54.938 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 46.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 720245 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |