7YQ8
Cryo-EM structure of human topoisomerase II beta in complex with DNA and etoposide
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000712 | biological_process | resolution of meiotic recombination intermediates |
| A | 0000792 | cellular_component | heterochromatin |
| A | 0000819 | biological_process | sister chromatid segregation |
| A | 0001764 | biological_process | neuron migration |
| A | 0003677 | molecular_function | DNA binding |
| A | 0003682 | molecular_function | chromatin binding |
| A | 0003916 | molecular_function | DNA topoisomerase activity |
| A | 0003918 | molecular_function | DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005730 | cellular_component | nucleolus |
| A | 0005829 | cellular_component | cytosol |
| A | 0006259 | biological_process | DNA metabolic process |
| A | 0006265 | biological_process | DNA topological change |
| A | 0007409 | biological_process | axonogenesis |
| A | 0030183 | biological_process | B cell differentiation |
| A | 0030900 | biological_process | forebrain development |
| A | 0034335 | molecular_function | DNA negative supercoiling activity |
| A | 0043021 | molecular_function | ribonucleoprotein complex binding |
| A | 0045870 | biological_process | positive regulation of single stranded viral RNA replication via double stranded DNA intermediate |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0070301 | biological_process | cellular response to hydrogen peroxide |
| A | 0071318 | biological_process | cellular response to ATP |
| A | 0090398 | biological_process | cellular senescence |
| A | 1990904 | cellular_component | ribonucleoprotein complex |
| A | 2001034 | biological_process | positive regulation of double-strand break repair via nonhomologous end joining |
| B | 0000712 | biological_process | resolution of meiotic recombination intermediates |
| B | 0000792 | cellular_component | heterochromatin |
| B | 0000819 | biological_process | sister chromatid segregation |
| B | 0001764 | biological_process | neuron migration |
| B | 0003677 | molecular_function | DNA binding |
| B | 0003682 | molecular_function | chromatin binding |
| B | 0003916 | molecular_function | DNA topoisomerase activity |
| B | 0003918 | molecular_function | DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005524 | molecular_function | ATP binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005730 | cellular_component | nucleolus |
| B | 0005829 | cellular_component | cytosol |
| B | 0006259 | biological_process | DNA metabolic process |
| B | 0006265 | biological_process | DNA topological change |
| B | 0007409 | biological_process | axonogenesis |
| B | 0030183 | biological_process | B cell differentiation |
| B | 0030900 | biological_process | forebrain development |
| B | 0034335 | molecular_function | DNA negative supercoiling activity |
| B | 0043021 | molecular_function | ribonucleoprotein complex binding |
| B | 0045870 | biological_process | positive regulation of single stranded viral RNA replication via double stranded DNA intermediate |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0070301 | biological_process | cellular response to hydrogen peroxide |
| B | 0071318 | biological_process | cellular response to ATP |
| B | 0090398 | biological_process | cellular senescence |
| B | 1990904 | cellular_component | ribonucleoprotein complex |
| B | 2001034 | biological_process | positive regulation of double-strand break repair via nonhomologous end joining |
Functional Information from PROSITE/UniProt
| site_id | PS00107 |
| Number of Residues | 22 |
| Details | PROTEIN_KINASE_ATP Protein kinases ATP-binding region signature. VGGGNGALTWvTlfdqnn............AAKK |
| Chain | Residue | Details |
| A | VAL13-LYS34 |
| site_id | PS00177 |
| Number of Residues | 9 |
| Details | TOPOISOMERASE_II DNA topoisomerase II signature. LTEGDSAKS |
| Chain | Residue | Details |
| A | LEU480-SER488 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | ACT_SITE: O-(5'-phospho-DNA)-tyrosine intermediate => ECO:0000255|PROSITE-ProRule:PRU01384, ECO:0000269|PubMed:21778401 |
| Chain | Residue | Details |
| A | TYR826 | |
| B | TYR826 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 10 |
| Details | BINDING: BINDING => ECO:0000250 |
| Chain | Residue | Details |
| A | ASN112 | |
| B | GLN397 | |
| A | ASN141 | |
| A | SER169 | |
| A | GLY182 | |
| A | GLN397 | |
| B | ASN112 | |
| B | ASN141 | |
| B | SER169 | |
| B | GLY182 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00995 |
| Chain | Residue | Details |
| A | GLU482 | |
| B | GLU482 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00995, ECO:0000269|PubMed:21778401 |
| Chain | Residue | Details |
| A | ASP562 | |
| A | ASP564 | |
| B | ASP562 | |
| B | ASP564 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 12 |
| Details | SITE: Interaction with DNA |
| Chain | Residue | Details |
| A | LYS510 | |
| B | LYS683 | |
| B | LYS744 | |
| B | TRP952 | |
| A | ASN513 | |
| A | ARG682 | |
| A | LYS683 | |
| A | LYS744 | |
| A | TRP952 | |
| B | LYS510 | |
| B | ASN513 | |
| B | ARG682 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | SITE: Interaction with DNA => ECO:0000255|PROSITE-ProRule:PRU00995 |
| Chain | Residue | Details |
| A | TYR778 | |
| B | TYR778 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | SITE: Transition state stabilizer |
| Chain | Residue | Details |
| A | ARG825 | |
| B | ARG825 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | SITE: Important for DNA bending; intercalates between base pairs of target DNA |
| Chain | Residue | Details |
| A | ILE877 | |
| B | ILE877 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | MOD_RES: N-acetylalanine => ECO:0000250|UniProtKB:Q64511 |
| Chain | Residue | Details |
| A | ALA2 | |
| B | ALA2 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q64511 |
| Chain | Residue | Details |
| A | LYS3 | |
| B | LYS3 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER1236 | |
| B | SER1236 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:19690332 |
| Chain | Residue | Details |
| A | THR1292 | |
| A | THR1403 | |
| B | THR1292 | |
| B | THR1403 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692 |
| Chain | Residue | Details |
| A | SER1336 | |
| A | SER1340 | |
| B | SER1336 | |
| B | SER1340 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692 |
| Chain | Residue | Details |
| A | SER1342 | |
| A | SER1344 | |
| B | SER1342 | |
| B | SER1344 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:21406692 |
| Chain | Residue | Details |
| A | SER1358 | |
| B | SER1358 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:Q64511 |
| Chain | Residue | Details |
| A | TYR1370 | |
| B | TYR1370 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332 |
| Chain | Residue | Details |
| A | SER1375 | |
| B | SER1375 |
| site_id | SWS_FT_FI18 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18220336, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | SER1400 | |
| A | SER1413 | |
| B | SER1400 | |
| B | SER1413 |
| site_id | SWS_FT_FI19 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:18669648 |
| Chain | Residue | Details |
| A | TYR1421 | |
| A | TYR1609 | |
| B | TYR1421 | |
| B | TYR1609 |
| site_id | SWS_FT_FI20 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER1424 | |
| A | SER1466 | |
| B | SER1424 | |
| B | SER1466 |
| site_id | SWS_FT_FI21 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692 |
| Chain | Residue | Details |
| A | SER1441 | |
| B | SER1441 |
| site_id | SWS_FT_FI22 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER1452 | |
| B | SER1452 |
| site_id | SWS_FT_FI23 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:17525332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER1454 | |
| B | SER1454 |
| site_id | SWS_FT_FI24 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:19690332 |
| Chain | Residue | Details |
| A | SER1461 | |
| A | SER1473 | |
| B | SER1461 | |
| B | SER1473 |
| site_id | SWS_FT_FI25 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231 |
| Chain | Residue | Details |
| A | SER1476 | |
| B | SER1476 |
| site_id | SWS_FT_FI26 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | SER1522 | |
| A | SER1524 | |
| B | SER1522 | |
| B | SER1524 |
| site_id | SWS_FT_FI27 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:20068231 |
| Chain | Residue | Details |
| A | SER1526 | |
| B | SER1526 |
| site_id | SWS_FT_FI28 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | SER1550 | |
| B | SER1550 |
| site_id | SWS_FT_FI29 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | SER1552 | |
| B | SER1552 |
| site_id | SWS_FT_FI30 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | THR1575 | |
| B | THR1575 |
| site_id | SWS_FT_FI31 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | SER1576 | |
| B | SER1576 |
| site_id | SWS_FT_FI32 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18220336, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | SER1581 | |
| B | SER1581 |
| site_id | SWS_FT_FI33 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:18669648 |
| Chain | Residue | Details |
| A | THR1592 | |
| B | THR1592 |
| site_id | SWS_FT_FI34 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648 |
| Chain | Residue | Details |
| A | SER1596 | |
| B | SER1596 |
| site_id | SWS_FT_FI35 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692 |
| Chain | Residue | Details |
| A | SER1613 | |
| B | SER1613 |
| site_id | SWS_FT_FI36 |
| Number of Residues | 44 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| A | LYS33 | |
| A | LYS635 | |
| A | LYS646 | |
| A | LYS676 | |
| A | LYS712 | |
| A | LYS1092 | |
| A | LYS1214 | |
| A | LYS1217 | |
| A | LYS1226 | |
| A | LYS1262 | |
| A | LYS1323 | |
| A | LYS1327 | |
| A | LYS1398 | |
| A | LYS1490 | |
| B | LYS33 | |
| B | LYS178 | |
| B | LYS228 | |
| B | LYS299 | |
| B | LYS367 | |
| B | LYS439 | |
| A | LYS178 | |
| B | LYS446 | |
| B | LYS600 | |
| B | LYS635 | |
| B | LYS646 | |
| B | LYS676 | |
| B | LYS712 | |
| B | LYS1092 | |
| B | LYS1214 | |
| B | LYS1217 | |
| B | LYS1226 | |
| A | LYS228 | |
| B | LYS1262 | |
| B | LYS1323 | |
| B | LYS1327 | |
| B | LYS1398 | |
| B | LYS1490 | |
| A | LYS299 | |
| A | LYS367 | |
| A | LYS439 | |
| A | LYS446 | |
| A | LYS600 |
| site_id | SWS_FT_FI37 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25218447 |
| Chain | Residue | Details |
| A | LYS34 | |
| B | LYS34 |
| site_id | SWS_FT_FI38 |
| Number of Residues | 10 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25772364, ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| A | LYS177 | |
| B | LYS643 | |
| A | LYS373 | |
| A | LYS437 | |
| A | LYS605 | |
| A | LYS643 | |
| B | LYS177 | |
| B | LYS373 | |
| B | LYS437 | |
| B | LYS605 |
| site_id | SWS_FT_FI39 |
| Number of Residues | 6 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25218447, ECO:0007744|PubMed:25772364, ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| A | LYS1227 | |
| A | LYS1440 | |
| A | LYS1456 | |
| B | LYS1227 | |
| B | LYS1440 | |
| B | LYS1456 |
| site_id | SWS_FT_FI40 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25755297, ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| A | LYS1250 | |
| B | LYS1250 |
| site_id | SWS_FT_FI41 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25218447, ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| A | LYS1271 | |
| B | LYS1271 |
