4CHT | pdb_00004cht

Crystal structure of the human topoisomerase III alpha-RMI1 complex with bound calcium ion

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B		e4chtB1	A: DEATH domain	X: 6-phosphogluconate dehydrogenase C-terminal domain-like	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: CblD	F:	ECOD (20:10:01)
A		e4chtA1	A: DEATH domain	X: 6-phosphogluconate dehydrogenase C-terminal domain-like	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: CblD	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.8.1020	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B	2.40.50.770	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RecQ-mediated genome instability protein Rmi1, C-terminal domain	CATH (4.3.0)
A	3.40.50.140	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	1.10.460.10	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	domain 2	CATH (4.3.0)
A	2.70.20.10	Mainly Beta	Distorted Sandwich	Topoisomerase I	domain 3	CATH (4.3.0)
A	1.10.290.10	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF08585	RMI1, N-terminal OB-fold domain (RMI1_N_C)	RMI1, N-terminal OB-fold domain	This is the OB-fold domain found at the N-terminal of RecQ-mediated genome instability protein 1 (RMI1), which forms a stable complex with Bloom syndrome protein BLM and DNA topoisomerase 3-alpha [1-3].	Domain
B	PF21000	RMI1, N-terminal helical domain (RMI1_N_N)	RMI1, N-terminal helical domain	The N-terminal domain of RecQ-mediated genome instability protein 1 carries an oligo-nucleotide-binding domain or OB-fold, and forms a stable complex with Bloom syndrome protein BLM and DNA topoisomerase 3-alpha [1-3]. At the very N-terminal, it has ...	The N-terminal domain of RecQ-mediated genome instability protein 1 carries an oligo-nucleotide-binding domain or OB-fold, and forms a stable complex with Bloom syndrome protein BLM and DNA topoisomerase 3-alpha [1-3]. At the very N-terminal, it has a 3-helix bundle, represented in this entry, which protrudes to one side of the structure and makes extensive hydrophobic contacts with the convex side of the beta-barrel [3].	Domain
A	PF01131	DNA topoisomerase (Topoisom_bac)	DNA topoisomerase	-	Family
A	PF01751	Toprim domain (Toprim)	Toprim domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	RECQ-MEDIATED GENOME INSTABILITY PROTEIN 1	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process resolution of DNA recombination intermediates DNA recombination reduction of food intake in response to dietary excess multicellular organismal process response to nutrient levels response to stimulus nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process resolution of DNA recombination intermediates DNA recombination reduction of food intake in response to dietary excess multicellular organismal process response to nutrient levels response to stimulus homeostatic process eating behavior feeding behavior behavior multicellular organismal-level homeostasis response to dietary excess energy homeostasis cellular response to stimulus double-strand break repair cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair sexual reproduction homologous recombination reproductive process resolution of meiotic recombination intermediates meiotic cell cycle process cellular component organization meiosis I meiotic nuclear division cell cycle cellular component organization or biogenesis reciprocal homologous recombination cell cycle process meiotic cell cycle organelle fission reciprocal meiotic recombination nuclear division organelle organization meiosis I cell cycle process developmental process multicellular organism growth developmental growth growth response to hexose response to monosaccharide response to carbohydrate response to glucose response to chemical response to oxygen-containing compound chemical homeostasis glucose homeostasis carbohydrate homeostasis	protein-containing complex intracellular anatomical structure catalytic complex intracellular membraneless organelle chromosome intracellular organelle cellular anatomical structure RecQ family helicase-topoisomerase III complex organelle membraneless organelle DNA helicase complex membrane-bounded organelle nucleus membrane-enclosed lumen protein-containing complex intracellular anatomical structure catalytic complex intracellular membraneless organelle chromosome intracellular organelle cellular anatomical structure RecQ family helicase-topoisomerase III complex organelle membraneless organelle DNA helicase complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear body nucleoplasm organelle lumen nuclear lumen
A	DNA TOPOISOMERASE 3-ALPHA	DNA binding binding nucleic acid binding nucleic acid conformation isomerase activity isomerase activity DNA topoisomerase type I (single strand cut, ATP-independent) activity catalytic activity, acting on DNA DNA topoisomerase activity catalytic activity, acting on a nucleic acid catalytic activity macromolecular conformation isomerase activity cation binding transition metal ion binding zinc ion binding DNA binding binding nucleic acid binding nucleic acid conformation isomerase activity isomerase activity DNA topoisomerase type I (single strand cut, ATP-independent) activity catalytic activity, acting on DNA DNA topoisomerase activity catalytic activity, acting on a nucleic acid catalytic activity macromolecular conformation isomerase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding single-stranded DNA binding	chromosome organization primary metabolic process DNA conformation change DNA metabolic process nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process DNA topological change organelle organization cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process DNA recombination chromosome organization primary metabolic process DNA conformation change DNA metabolic process nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process DNA topological change organelle organization cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process DNA recombination resolution of DNA recombination intermediates chromosome separation cell cycle chromosome segregation cell cycle process cellular response to stimulus double-strand break repair response to stimulus cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair mitochondrial DNA metabolic process sexual reproduction reproductive process meiotic cell cycle	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex intracellular membraneless organelle chromosome RecQ family helicase-topoisomerase III complex membraneless organelle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex intracellular membraneless organelle chromosome RecQ family helicase-topoisomerase III complex membraneless organelle DNA helicase complex nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen mitochondrial matrix nuclear body PML body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR013894	RecQ mediated genome instability protein 1, OB-fold domain	Domain
B	IPR042470	RecQ mediated genome instability protein, N-terminal OB-fold domain superfamily	Homologous Superfamily
B	IPR032199	RecQ-mediated genome instability protein 1, C-terminal OB-fold domain	Domain
B	IPR049363	RMI1, N-terminal domain	Domain
B	IPR044881	RecQ-mediated genome instability protein 1, N-terminal helical domain superfamily	Homologous Superfamily
A	IPR013498	DNA topoisomerase, type IA, zn finger	Domain
A	IPR003601	DNA topoisomerase, type IA, domain 2	Domain
A	IPR010666	Zinc finger, GRF-type	Domain
A	IPR000380	DNA topoisomerase, type IA	Family
A	IPR013826	DNA topoisomerase, type IA, central region, subdomain 3	Homologous Superfamily
A	IPR006171	TOPRIM domain	Domain
A	IPR013497	DNA topoisomerase, type IA, central	Domain
A	IPR003602	DNA topoisomerase, type IA, DNA-binding domain	Domain
A	IPR023405	DNA topoisomerase, type IA, core domain	Homologous Superfamily
A	IPR013825	DNA topoisomerase, type IA, central region, subdomain 2	Homologous Superfamily
A	IPR023406	DNA topoisomerase, type IA, active site	Active Site
A	IPR034144	DNA topoisomerase 3-like, TOPRIM domain	Domain
A	IPR013824	DNA topoisomerase, type IA, central region, subdomain 1	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q9H9A7	attention deficit hyperactivity disorder, inattentive type breast cancer hepatocellular carcinoma malignant ependymoma non-small cell lung carcinoma atypical teratoid rhabdoid tumor breast carcinoma invasive ductal breast carcinoma malignant mesothelioma pancreatic intraductal papillary-mucinous neoplasm Bloom syndrome ductal breast carcinoma in situ lung cancer medulloblastoma primitive neuroectodermal tumor
A	Pharos: Q13472	attention deficit hyperactivity disorder, inattentive type microcephaly, growth restriction, and increased sister chromatid exchange 2 progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 5 Bloom syndrome osteosarcoma psoriasis malignant mesothelioma progressive external ophthalmoplegia

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.