Cryo-EM structure of human topoisomerase II beta in complex with DNA and etoposide

2025-06-25 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY em_admin em_software pdbx_entry_details _em_admin.last_update _em_software.name _pdbx_entry_details.has_protein_modification EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name PDBj PDBj 2022-08-05 2024-01-03 2024-01-03 2025-06-25 Japan Society for the Promotion of Science (JSPS) JP20H05690 Japan Cryo-EM structure of human topoisomerase II beta in complex with DNA and etoposide Naganuma M Ehara H Kim D Nakagawa R Cong A Bu H Jeong J Jang J Schellenberg MJ Bunch H Sekine S Topoisomerase, Etoposide, DNA, ISOMERASE, ISOMERASE-DNA complex Bunch H Kim D Naganuma M Nakagawa R Cong A Jeong J Ehara H Vu H Chang JH Schellenberg MJ Sekine SI ERK2-topoisomerase II regulatory axis is important for gene activation in immediate early genes. Nat Commun UK 14 8341 8341 2023 38097570 doi:10.1038/s41467-023-44089-y 2041-1723 7yq8 FULLOVERLAP Ternary complex of human topoisomerase II beta with DNA and etoposide Ternary complex of human topoisomerase II beta with DNA and etoposide 0 1 2 3 human topoisomerase II beta 1 1 Homo sapiens DNA 1 2 3 DNA topoisomerase 2-beta Homo sapiens 0.18354225 2 Homo sapiens LEVO MAKSGGCGAGAGVGGGNGALTWVTLFDQNNAAKKEESETANKNDSSKKLSVERVYQKKTQLEHILLRPDTYIGSVEPLTQ FMWVYDEDVGMNCREVTFVPGLYKIFDEILVNAADNKQRDKNMTCIKVSIDPESNIISIWNNGKGIPVVEHKVEKVYVPA LIFGQLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTKFTVETACKEYKHSFKQTWMNNMMKTSEAKIKHFDGEDYTCITF QPDLSKFKMEKLDKDIVALMTRRAYDLAGSCRGVKVMFNGKKLPVNGFRSYVDLYVKDKLDETGVALKVIHELANERWDV CLTLSEKGFQQISFVNSIATTKGGRHVDYVVDQVVGKLIEVVKKKNKAGVSVKPFQVKNHIWVFINCLIENPTFDSQTKE NMTLQPKSFGSKCQLSEKFFKAASNCGIVESILNWVKFKAQTQLNKKCSSVKYSKIKGIPKLDDANDAGGKHSLECTLIL TEGDSAKSLAVSGLGVIGRDRYGVFPLRGKILNVREASHKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLRYGKIMIM TDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITPIVKASKNKQELSFYSIPEFDEWKKHIENQKAWKIKYYKGLGTS TAKEAKEYFADMERHRILFRYAGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQRRLHGLPEQFLYGTATKHLTYNDFI NKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCFKRNDKREVKVAQLAGSVAEMSAYHHGEQALMMTIVNLAQNFVGSN NINLLQPIGQFGTRLHGGKDAASPRYIFTMLSTLARLLFPAVDDNLLKFLYDDNQRVEPEWYIPIIPMVLINGAEGIGTG WACKLPNYDAREIVNNVRRMLDGLDPHPMLPNYKNFKGTIQELGQNQYAVSGEIFVVDRNTVEITELPVRTWTQVYKEQV LEPMLNGTDKTPALISDYKEYHTDTTVKFVVKMTEEKLAQAEAAGLHKVFKLQTTLTCNSMVLFDHMGCLKKYETVQDIL KEFFDLRLSYYGLRKEWLVGMLGAESTKLNNQARFILEKIQGKITIENRSKKDLIQMLVQRGYESDPVKAWKEAQEKAAE EDETQNQHDDSSSDSGTPSGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVNDLKRKSPSDLWKEDLAAFVEELDKVE SQEREDVLAGMSGKAIKGKVGKPKVKKLQLEETMPSPYGRRIIPEITAMKADASKKLLKKKKGDLDTAAVKVEFDEEFSG APVEGAGEEALTPSVPINKGPKPKREKKEPGTRVRKTPTSSGKPSAKKVKKRNPWSDDESKSESDLEETEPVVIPRDSLL RRAAAERPKYTFDFSEEEDDDADDDDDDNNDLEELKVKASPITNDGEDEFVPSDGLDKDEYTFSPGKSKATPEKSLHDKK SQDFGNLFSFPSYSQKSEDDSAKFDSNEEDSASVFSPSFGLKQTDKVPSKTVAAKKGKPSSDTVPKPKRAPKQKKVVEAV NSDSDSEFGIPKKTTTPKGKGRGAKKRKASGSENEGDYNPGRKTSKTTSKKPKKTSFDQDSDVDIFPSDFPTEPPSLPRT GRARKEVKYFAESDEEEDDVDFAMFN Q02880 5.6.2.2 50-mer DNA Homo sapiens 0.015449866 2 (DG)(DA)(DG)(DT)(DC)(DG)(DC)(DG)(DA)(DG)(DA)(DG)(DA)(DT)(DC)(DC)(DC)(DA)(DG)(DC) (DG)(DC)(DG)(DC)(DA)(DG)(DA)(DA)(DC)(DT)(DT)(DG)(DG)(DG)(DG)(DA)(DG)(DC)(DC)(DG) (DC)(DC)(DG)(DC)(DC)(DG)(DC)(DC)(DA)(DT) DNA 50-mer DNA Homo sapiens 0.015364772999999998 2 (DA)(DT)(DG)(DG)(DC)(DG)(DG)(DC)(DG)(DG)(DC)(DG)(DG)(DC)(DT)(DC)(DC)(DC)(DC)(DA) (DA)(DG)(DT)(DT)(DC)(DT)(DG)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DG)(DG)(DA)(DT)(DC)(DT) (DC)(DT)(DC)(DG)(DC)(DG)(DA)(DC)(DT)(DC) DNA MAGNESIUM ION 2.4305e-05 2 MG (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside 0.000588557 2 EVP singleParticle particle 8.0 ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 2.5 GATAN K3 BIOQUANTUM (6k x 4k) 49.0 1 NONE C2 3.9 FSC 0.143 CUT-OFF 26067 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_34022.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 249.0 249.0 249.0 90.0 90.0 90.0 X Y Z -0.02671669 0.06579608 0.00020672106 0.0026507408 1.245 1.245 1.245 0.0125 AUTHOR ::::EMDATABANK.org::::EMD-34022:::: emd_34022_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 249.0 249.0 249.0 90.0 90.0 90.0 X Y Z -0.052868124 0.09281062 0.00020575333 0.005164188 1.245 1.245 1.245 AUTHOR ::::EMDATABANK.org::::EMD-34022:::: emd_34022_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 249.0 249.0 249.0 90.0 90.0 90.0 X Y Z -0.050737977 0.09616266 0.00020756011 0.0052046566 1.245 1.245 1.245 AUTHOR ::::EMDATABANK.org::::EMD-34022::::