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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

6ZY5

Cryo-EM structure of the Human topoisomerase II alpha DNA-binding/cleavage domain in State 1

Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0000228cellular_componentnuclear chromosome
A0000287molecular_functionmagnesium ion binding
A0000712biological_processresolution of meiotic recombination intermediates
A0000775cellular_componentchromosome, centromeric region
A0000793cellular_componentcondensed chromosome
A0000819biological_processsister chromatid segregation
A0003677molecular_functionDNA binding
A0003682molecular_functionchromatin binding
A0003723molecular_functionRNA binding
A0003916molecular_functionDNA topoisomerase activity
A0003918molecular_functionDNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
A0005080molecular_functionprotein kinase C binding
A0005515molecular_functionprotein binding
A0005524molecular_functionATP binding
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0005730cellular_componentnucleolus
A0005737cellular_componentcytoplasm
A0005814cellular_componentcentriole
A0006259biological_processDNA metabolic process
A0006265biological_processDNA topological change
A0006325biological_processchromatin organization
A0006974biological_processDNA damage response
A0007059biological_processchromosome segregation
A0007143biological_processfemale meiotic nuclear division
A0008094molecular_functionATP-dependent activity, acting on DNA
A0008301molecular_functionDNA binding, bending
A0009330cellular_componentDNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex
A0016853molecular_functionisomerase activity
A0030263biological_processapoptotic chromosome condensation
A0032991cellular_componentprotein-containing complex
A0042752biological_processregulation of circadian rhythm
A0042803molecular_functionprotein homodimerization activity
A0043065biological_processpositive regulation of apoptotic process
A0043130molecular_functionubiquitin binding
A0045870biological_processpositive regulation of single stranded viral RNA replication via double stranded DNA intermediate
A0046872molecular_functionmetal ion binding
A0046982molecular_functionprotein heterodimerization activity
A0048511biological_processrhythmic process
A1990904cellular_componentribonucleoprotein complex
B0000166molecular_functionnucleotide binding
B0000228cellular_componentnuclear chromosome
B0000287molecular_functionmagnesium ion binding
B0000712biological_processresolution of meiotic recombination intermediates
B0000775cellular_componentchromosome, centromeric region
B0000793cellular_componentcondensed chromosome
B0000819biological_processsister chromatid segregation
B0003677molecular_functionDNA binding
B0003682molecular_functionchromatin binding
B0003723molecular_functionRNA binding
B0003916molecular_functionDNA topoisomerase activity
B0003918molecular_functionDNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
B0005080molecular_functionprotein kinase C binding
B0005515molecular_functionprotein binding
B0005524molecular_functionATP binding
B0005634cellular_componentnucleus
B0005654cellular_componentnucleoplasm
B0005730cellular_componentnucleolus
B0005737cellular_componentcytoplasm
B0005814cellular_componentcentriole
B0006259biological_processDNA metabolic process
B0006265biological_processDNA topological change
B0006325biological_processchromatin organization
B0006974biological_processDNA damage response
B0007059biological_processchromosome segregation
B0007143biological_processfemale meiotic nuclear division
B0008094molecular_functionATP-dependent activity, acting on DNA
B0008301molecular_functionDNA binding, bending
B0009330cellular_componentDNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex
B0016853molecular_functionisomerase activity
B0030263biological_processapoptotic chromosome condensation
B0032991cellular_componentprotein-containing complex
B0042752biological_processregulation of circadian rhythm
B0042803molecular_functionprotein homodimerization activity
B0043065biological_processpositive regulation of apoptotic process
B0043130molecular_functionubiquitin binding
B0045870biological_processpositive regulation of single stranded viral RNA replication via double stranded DNA intermediate
B0046872molecular_functionmetal ion binding
B0046982molecular_functionprotein heterodimerization activity
B0048511biological_processrhythmic process
B1990904cellular_componentribonucleoprotein complex
Functional Information from PROSITE/UniProt
site_idPS00177
Number of Residues9
DetailsTOPOISOMERASE_II DNA topoisomerase II signature. LTEGDSAKT
ChainResidueDetails
BLEU459-THR467
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues234
DetailsDomain: {"description":"Toprim","evidences":[{"source":"PROSITE-ProRule","id":"PRU00995","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues18
DetailsRegion: {"description":"Interaction with DNA","evidences":[{"source":"PubMed","id":"22841979","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues20
DetailsMotif: {"description":"Nuclear export signal"}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues2
DetailsActive site: {"description":"O-(5'-phospho-DNA)-tyrosine intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU01384","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues2
DetailsBinding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00995","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"22841979","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues2
DetailsSite: {"description":"Interaction with DNA","evidences":[{"source":"PROSITE-ProRule","id":"PRU00995","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues14
DetailsSite: {"description":"Interaction with DNA","evidences":[{"source":"PubMed","id":"22841979","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues2
DetailsSite: {"description":"Transition state stabilizer","evidences":[{"source":"UniProtKB","id":"P06786","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues2
DetailsSite: {"description":"Important for DNA bending; intercalates between base pairs of target DNA","evidences":[{"source":"UniProtKB","id":"P06786","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues2
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"16964243","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"17081983","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"18691976","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"21406692","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues26
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues10
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"25772364","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

247536

PDB entries from 2026-01-14

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