6ZY5 | pdb_00006zy5

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

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth A]	DNA_topoisoIV_1st	e6zy5A2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DNA_topoisoIV_1st	ECOD (1.6)
F [auth A]	DNA_topoisoIV_3rd	e6zy5A4	A: alpha bundles	X: alpha-helical domain in type II DNA topoisomerase (From Topology)	H: alpha-helical domain in type II DNA topoisomerase (From Topology)	T: alpha-helical domain in type II DNA topoisomerase	F: DNA_topoisoIV_3rd	ECOD (1.6)
F [auth A]	TOPRIM_C	e6zy5A1	A: a+b two layers	X: SSHS domain	H: SSHS domain in type II DNA topoisomerase (From Topology)	T: SSHS domain in type II DNA topoisomerase	F: TOPRIM_C	ECOD (1.6)
F [auth A]	DNA_topoisoIV_2nd_1	e6zy5A3	A: a+b two layers	X: a+b domain in type II DNA topoisomerase (From Topology)	H: a+b domain in type II DNA topoisomerase (From Topology)	T: a+b domain in type II DNA topoisomerase	F: DNA_topoisoIV_2nd_1	ECOD (1.6)
F [auth A]	DNA_gyraseB_C	e6zy5A5	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: DNA_gyraseB_C	ECOD (1.6)
A [auth B]	DNA_topoisoIV_1st	e6zy5B5	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DNA_topoisoIV_1st	ECOD (1.6)
A [auth B]	DNA_topoisoIV_3rd	e6zy5B1	A: alpha bundles	X: alpha-helical domain in type II DNA topoisomerase (From Topology)	H: alpha-helical domain in type II DNA topoisomerase (From Topology)	T: alpha-helical domain in type II DNA topoisomerase	F: DNA_topoisoIV_3rd	ECOD (1.6)
A [auth B]	TOPRIM_C	e6zy5B3	A: a+b two layers	X: SSHS domain	H: SSHS domain in type II DNA topoisomerase (From Topology)	T: SSHS domain in type II DNA topoisomerase	F: TOPRIM_C	ECOD (1.6)
A [auth B]	DNA_topoisoIV_2nd_1	e6zy5B4	A: a+b two layers	X: a+b domain in type II DNA topoisomerase (From Topology)	H: a+b domain in type II DNA topoisomerase (From Topology)	T: a+b domain in type II DNA topoisomerase	F: DNA_topoisoIV_2nd_1	ECOD (1.6)
A [auth B]	DNA_gyraseB_C	e6zy5B2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: DNA_gyraseB_C	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], F [auth A]	PF01751	Toprim domain (Toprim)	Toprim domain	-	Family
A [auth B], F [auth A]	PF16898	C-terminal associated domain of TOPRIM (TOPRIM_C)	C-terminal associated domain of TOPRIM	-	Family
A [auth B], F [auth A]	PF00521	DNA gyrase/topoisomerase IV, subunit A (DNA_topoisoIV)	DNA gyrase/topoisomerase IV, subunit A	This entry represents a domain found in type IIA topoisomerases, such as bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA), and mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that r ...	This entry represents a domain found in type IIA topoisomerases, such as bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA), and mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA topology by catalysing the concerted breakage and rejoining of DNA strands during normal cellular growth [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], F [auth A]	DNA topoisomerase 2-alpha	ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity ATP-dependent activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity ATP-dependent activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding chromatin binding protein heterodimerization activity protein binding protein dimerization activity ubiquitin binding ubiquitin-like protein binding RNA binding cation binding magnesium ion binding metal ion binding identical protein binding protein homodimerization activity kinase binding protein kinase C binding enzyme binding protein kinase binding DNA binding, bending nucleic acid conformation isomerase activity isomerase activity DNA topoisomerase activity DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity macromolecular conformation isomerase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process multicellular organism development multicellular organismal process embryonic cleavage anatomical structure development cell division embryo development regulation of single stranded viral RNA replication via double stranded DNA intermediate cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process multicellular organism development multicellular organismal process embryonic cleavage anatomical structure development cell division embryo development regulation of single stranded viral RNA replication via double stranded DNA intermediate regulation of cellular process positive regulation of biological process RNA metabolic process viral life cycle positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of single stranded viral RNA replication via double stranded DNA intermediate positive regulation of biosynthetic process viral RNA genome replication viral process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process positive regulation of viral genome replication positive regulation of viral process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process single stranded viral RNA replication via double stranded DNA intermediate nucleic acid metabolic process positive regulation of RNA metabolic process regulation of viral life cycle regulation of viral process biosynthetic process viral genome replication positive regulation of RNA biosynthetic process regulation of viral genome replication metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process cell cycle chromosome segregation cell cycle process positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death chromosome organization DNA conformation change DNA metabolic process cellular component organization DNA topological change organelle organization cellular component organization or biogenesis positive regulation of DNA-templated transcription DNA-templated transcription transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II gene expression regulation of gene expression regulation of DNA-templated transcription chromatin organization rhythmic process circadian rhythm regulation of circadian rhythm sexual reproduction homologous recombination reproductive process resolution of meiotic recombination intermediates meiotic cell cycle process meiosis I meiotic nuclear division reciprocal homologous recombination meiotic cell cycle DNA recombination organelle fission reciprocal meiotic recombination nuclear division meiosis I cell cycle process multicellular organismal reproductive process female gamete generation gamete generation female meiotic nuclear division cellular component disassembly execution phase of apoptosis apoptotic chromosome condensation chromosome condensation cellular component disassembly involved in execution phase of apoptosis apoptotic nuclear changes nuclear chromosome segregation sister chromatid segregation cellular developmental process hemopoiesis cell differentiation cell development hematopoietic progenitor cell differentiation	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle male germ cell nucleus nucleus germ cell nucleus intracellular membrane-bounded organelle DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex protein-containing complex catalytic complex membrane-enclosed lumen cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle male germ cell nucleus nucleus germ cell nucleus intracellular membrane-bounded organelle DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex protein-containing complex catalytic complex membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen chromosome condensed chromosome chromosome, centromeric region chromosomal region nucleoplasm ribonucleoprotein complex
B [auth D], D [auth F]	DNA (5'-D(CPGPCPGPCPAPTPCPGPTPCPAPTPCPCPTP*C)-3')	-	-	-
C [auth E], E [auth C]	DNA (5'-D(GPAPGPGPAPTPGPAPCPGPAPTP*G)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], F [auth A]	IPR013506	DNA topoisomerase, type IIA, subunit B, domain 2	Domain
A [auth B], F [auth A]	IPR006171	TOPRIM domain	Domain
A [auth B], F [auth A]	IPR003594	Histidine kinase/HSP90-like ATPase domain	Domain
A [auth B], F [auth A]	IPR034157	DNA topoisomerase 2, TOPRIM domain	Domain
A [auth B], F [auth A]	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A [auth B], F [auth A]	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily
A [auth B], F [auth A]	IPR031660	C-terminal associated domain of TOPRIM	Domain
A [auth B], F [auth A]	IPR002205	DNA topoisomerase, type IIA, domain A	Domain
A [auth B], F [auth A]	IPR001154	DNA topoisomerase II, eukaryotic-type	Family
A [auth B], F [auth A]	IPR018522	DNA topoisomerase, type IIA, conserved site	Conserved Site
A [auth B], F [auth A]	IPR013760	DNA topoisomerase, type IIA-like domain superfamily	Homologous Superfamily
A [auth B], F [auth A]	IPR013758	DNA topoisomerase, type IIA, domain A, alpha-beta	Homologous Superfamily
A [auth B], F [auth A]	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
A [auth B], F [auth A]	IPR001241	DNA topoisomerase, type IIA	Family
A [auth B], F [auth A]	IPR012542	DTHCT	Domain
A [auth B], F [auth A]	IPR013757	DNA topoisomerase, type IIA, alpha-helical domain superfamily	Homologous Superfamily
A [auth B], F [auth A]	IPR013759	DNA topoisomerase, type IIA, subunit B, C-terminal	Homologous Superfamily
A [auth B], F [auth A]	IPR050634	DNA Topoisomerase II	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B], F [auth A]	Pharos: P11388	adrenal cortex carcinoma breast carcinoma malignant glioma polycystic ovary syndrome neuroblastoma ovarian cancer leukemia prostate cancer lung adenocarcinoma breast cancer mixed glioma adenoid cystic carcinoma salivary gland adenoid cystic carcinoma Disease Exacerbation small cell lung carcinoma adrenal cortex carcinoma breast carcinoma malignant glioma polycystic ovary syndrome neuroblastoma ovarian cancer leukemia prostate cancer lung adenocarcinoma breast cancer mixed glioma adenoid cystic carcinoma salivary gland adenoid cystic carcinoma Disease Exacerbation small cell lung carcinoma thyroid cancer ductal breast carcinoma in situ urinary bladder cancer esophageal adenocarcinoma nasopharyngeal carcinoma glioma Hodgkins lymphoma acute lymphoblastic leukemia pancreatic intraductal papillary-mucinous neoplasm acute promyelocytic leukemia plasma cell myeloma adrenal carcinoma atopic eczema bone osteosarcoma malignant colon neoplasm Burkitt lymphoma salivary gland cancer cystic fibrosis sinusitis medulloblastoma endometriosis hepatocellular carcinoma non-small cell lung carcinoma IgA glomerulonephritis pancreatic ductal adenocarcinoma acute monocytic leukemia invasive ductal breast carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia kidney Wilms tumor atypical teratoid rhabdoid tumor malignant ependymoma relapsing-remitting multiple sclerosis cancer Sjogren syndrome testicular cancer ulcerative colitis glioblastoma oligodendroglioma interstitial cystitis pancreatic intraductal papillary-mucinous carcinoma acute myeloid leukemia Kaposi's sarcoma pilocytic astrocytoma large cell medulloblastoma primitive neuroectodermal tumor astrocytic tumor lung cancer psoriasis malignant pancreatic neoplasm

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.