3AL3 | pdb_00003al3

Crystal Structure of TopBP1 BRCT7/8-BACH1 peptide complex

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
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PTCB-BRCT	e3al3A5	A: a/b three-layered sandwiches	X: BRCT domain (From Topology)	H: BRCT domain (From Topology)	T: BRCT domain	F: PTCB-BRCT	ECOD (1.6)
A	BRCT_2_2	e3al3A6	A: a/b three-layered sandwiches	X: BRCT domain (From Topology)	H: BRCT domain (From Topology)	T: BRCT domain	F: BRCT_2_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.10190	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	BRCT domain	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF23294	TopBP1/SLF1, BRCT domain (BRCT_TopB1_SLF1)	TopBP1/SLF1, BRCT domain	This entry represents a BRCT domain found in TopBP1 (also known as DNA topoisomerase II-beta-binding protein 1) and SLF1 (SMC5-SMC6 complex localization factor protein 1). TopBP1 functions in DNA replication and damage response. It binds double-stran ...	This entry represents a BRCT domain found in TopBP1 (also known as DNA topoisomerase II-beta-binding protein 1) and SLF1 (SMC5-SMC6 complex localization factor protein 1). TopBP1 functions in DNA replication and damage response. It binds double-stranded DNA breaks and nicks as well as single-stranded DNA [1]. SLF1 plays a role in the DNA damage response (DDR) pathway by regulating postreplication repair of UV-damaged DNA and genomic stability maintenance [2]. This entry corresponds to the eight BRCT domain of TopBP1 and the second one in SLF1.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Peptide of Fanconi anemia group J protein	nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity ATP-dependent activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity macromolecular conformation isomerase activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity ATP-dependent activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity macromolecular conformation isomerase activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule 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 DNA binding nucleic acid binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity, acting on RNA RNA helicase activity ATP-dependent activity, acting on RNA cation binding metal ion binding	developmental process multicellular organismal process reproductive system development gonad development tube development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics seminiferous tubule development developmental process multicellular organismal process reproductive system development gonad development tube development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics seminiferous tubule development anatomical structure development reproductive structure development system development cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress protein-DNA covalent cross-linking repair metabolic process cellular process macromolecule metabolic process DNA repair meiotic chromosome segregation homologous recombination sexual reproduction meiotic cell cycle process cellular component organization cellular component biogenesis cellular component assembly meiosis I meiotic nuclear division cell cycle cellular component organization or biogenesis reciprocal homologous recombination chromosome segregation cell cycle process DNA recombination meiotic cell cycle organelle fission chiasma assembly chromosome organization reciprocal meiotic recombination chromosome organization involved in meiotic cell cycle nuclear division organelle organization meiosis I cell cycle process homologous chromosome pairing at meiosis nuclear chromosome segregation homologous chromosome segregation spermatid development spermatid differentiation cellular developmental process spermatogenesis multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism gamete generation male gamete generation cell differentiation germ cell development spermatogonial cell division cell division nucleotide-excision repair regulation of cellular process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process double-strand break repair double-strand break repair involved in meiotic recombination DNA double-strand break processing meiotic DNA double-strand break processing meiotic DNA double-strand break processing involved in reciprocal meiotic recombination DNA damage checkpoint signaling regulation of cell cycle phase transition signaling negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction cell communication negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction regulation of cell cycle regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling signal transduction in response to DNA damage	membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane cytoplasm membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex BRCA1-B complex nuclear protein-containing complex membraneless organelle replication fork intracellular membraneless organelle chromosome
A	DNA topoisomerase 2-binding protein 1	chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding binding nucleic acid binding enzyme regulator activity protein serine/threonine kinase activator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding binding nucleic acid binding enzyme regulator activity protein serine/threonine kinase activator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity identical protein binding protein binding phosphorylation-dependent protein binding modification-dependent protein binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process regulation of cell cycle phase transition signaling G2/M transition of mitotic cell cycle negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process regulation of cell cycle phase transition signaling G2/M transition of mitotic cell cycle negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle cell communication mitotic G2/M transition checkpoint regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction cell cycle DNA replication checkpoint signaling regulation of cell cycle cell cycle process cell cycle G2/M phase transition regulation of biological process mitotic DNA replication checkpoint signaling negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process biological regulation DNA integrity checkpoint signaling regulation of cell cycle G2/M phase transition negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic cell cycle process negative regulation of cell cycle G2/M phase transition negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process double-strand break repair via classical nonhomologous end joining double-strand break repair double-strand break repair via nonhomologous end joining DNA repair cellular component organization organelle organization chromosome organization cellular component organization or biogenesis localization protein localization to chromosome protein localization to organelle macromolecule localization protein localization to site of double-strand break intracellular protein localization homologous recombination DNA recombination response to ionizing radiation response to radiation response to abiotic stimulus DNA damage checkpoint signaling mitotic G2 DNA damage checkpoint signaling mitotic DNA damage checkpoint signaling signal transduction in response to DNA damage recombinational repair double-strand break repair via homologous recombination double-strand break repair via alternative nonhomologous end joining broken chromosome clustering	intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton membrane-bounded organelle condensed nuclear chromosome nucleus membrane-enclosed lumen intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton membrane-bounded organelle condensed nuclear chromosome nucleus membrane-enclosed lumen nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen condensed chromosome nuclear lumen actin cytoskeleton centrosome microtubule organizing center cell periphery plasma membrane membrane cytoplasm nucleoplasm protein-containing complex BRCA1-B complex nuclear protein-containing complex male germ cell nucleus germ cell nucleus site of double-strand break site of DNA damage nuclear body PML body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR045028	Helicase superfamily 1/2, DinG/Rad3-like	Family
B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
B	IPR006554	Helicase-like, DEXD box c2 type	Domain
B	IPR006555	ATP-dependent helicase, C-terminal	Domain
B	IPR010614	RAD3-like helicase, DEAD	Domain
B	IPR014013	Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type	Domain
B	IPR013020	ATP-dependent helicase Rad3/Chl1-like	Family
A	IPR001357	BRCT domain	Domain
A	IPR036420	BRCT domain superfamily	Homologous Superfamily
A	IPR035960	Secretoglobin superfamily	Homologous Superfamily
A	IPR049936	TopBP1, eighth BRCT domain	Domain
A	IPR044737	TopBP1, first BRCT domain	Domain
A	IPR049542	TopBP1-like, BRCT0 domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q9BX63	Fanconi anemia breast cancer ovarian cancer Fanconi anemia complementation group J ovarian carcinoma breast carcinoma hematopoietic and lymphoid system neoplasm Sjogren syndrome inherited aplastic anemia large cell medulloblastoma malignant ependymoma acute myeloid leukemia Malignant neoplasm of breast aplastic anemia cancer Fanconi anemia breast cancer ovarian cancer Fanconi anemia complementation group J ovarian carcinoma breast carcinoma hematopoietic and lymphoid system neoplasm Sjogren syndrome inherited aplastic anemia large cell medulloblastoma malignant ependymoma acute myeloid leukemia Malignant neoplasm of breast aplastic anemia cancer non-small cell lung carcinoma ductal breast carcinoma in situ familial prostate carcinoma pancreatic intraductal papillary-mucinous neoplasm glioblastoma psoriasis Warsaw breakage syndrome hereditary breast carcinoma intellectual disability leukemia malignant glioma adrenal cortex carcinoma atypical teratoid rhabdoid tumor medulloblastoma congenital anemia osteosarcoma ovarian neoplasm head and neck cancer hereditary breast ovarian cancer syndrome invasive ductal breast carcinoma lung adenocarcinoma malignant mesothelioma anemia breast adenocarcinoma nasopharyngeal carcinoma neurofibromatosis type 1 esophageal atresia/tracheoesophageal fistula pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor
A	Pharos: Q92547	B-cell chronic lymphocytic leukemia lymphoplasmacytic lymphoma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm diabetes mellitus malignant colon neoplasm non-small cell lung carcinoma lung cancer malignant mesothelioma ovarian cancer

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	TPO	Parent Component: THR RESID: AA0038 PSI-MOD : O-phospho-L-threonine MOD:00047

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.