3UEO | pdb_00003ueo

Crystal structure of TopBP1 BRCT4/5 domains in complex with a phospho-peptide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	BRCT-2 domain-like	8080041	4004711	SCOP2 (2022-06-29)
A	SCOP2 Family	BRCT-2 domain-like	8092285	4004711	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	BRCT domain-like	8092286	3000159	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	BRCT domain-like	8092287	3000159	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	BRCT domain-like	8092286	3000159	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	BRCT domain-like	8092287	3000159	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	BRCT domain-like	8092287	3000159	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	BRCT domain-like	8092286	3000159	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	BRCT domain-like	8092286	3000159	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	BRCT domain-like	8092287	3000159	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PTCB-BRCT	e3ueoA3	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)
B	PTCB-BRCT	e3ueoB3	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)
C	PTCB-BRCT	e3ueoC3	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)
D	PTCB-BRCT	e3ueoD3	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)

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 (4.3.0)
B	3.40.50.10190	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	BRCT domain	CATH (4.3.0)
C	3.40.50.10190	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	BRCT domain	CATH (4.3.0)
D	3.40.50.10190	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	BRCT domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00533	BRCA1 C Terminus (BRCT) domain (BRCT)	BRCA1 C Terminus (BRCT) domain	The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- ...	The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs [2]. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilised head-to-tail BRCT-BRCT oligomerisation mode [3]. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F	phospho-peptide	chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity histone reader activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process metabolic process macromolecule metabolic process DNA repair regulation of cellular process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process metabolic process macromolecule metabolic process DNA repair regulation of cellular process 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 cell cycle DNA replication checkpoint signaling regulation of cell cycle cell cycle process regulation of biological process regulation of cell cycle process biological regulation DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling localization protein localization to chromosome protein localization to organelle macromolecule localization protein localization to site of double-strand break intracellular protein localization DNA damage checkpoint signaling mitotic cell cycle negative regulation of mitotic cell cycle regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling mitotic intra-S DNA damage checkpoint signaling mitotic cell cycle checkpoint signaling mitotic cell cycle process signal transduction in response to DNA damage	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction intracellular organelle intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome site of double-strand break site of DNA damage membrane-bounded organelle cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction intracellular organelle intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome site of double-strand break site of DNA damage membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear body nucleoplasm organelle lumen nuclear lumen
A, B, C, D	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
E, F	IPR008984	SMAD/FHA domain superfamily	Homologous Superfamily
E, F	IPR000253	Forkhead-associated (FHA) domain	Domain
E, F	IPR051579	DNA Damage Response and Transcriptional Regulator	Family
E, F	IPR001357	BRCT domain	Domain
E, F	IPR036420	BRCT domain superfamily	Homologous Superfamily
A, B, C, D	IPR001357	BRCT domain	Domain
A, B, C, D	IPR036420	BRCT domain superfamily	Homologous Superfamily
A, B, C, D	IPR035960	Secretoglobin superfamily	Homologous Superfamily
A, B, C, D	IPR049936	TopBP1, eighth BRCT domain	Domain
A, B, C, D	IPR044737	TopBP1, first BRCT domain	Domain
A, B, C, D	IPR049542	TopBP1-like, BRCT0 domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F	Pharos: Q14676	psoriatic arthritis age-related macular degeneration cervical cancer cutaneous lupus erythematosus gastric carcinoma lymphoplasmacytic lymphoma osteosarcoma prostate carcinoma astrocytic tumor chronic obstructive pulmonary disease dermatomyositis Hashimoto thyroiditis malignant mesothelioma ovarian cancer psoriasis psoriatic arthritis age-related macular degeneration cervical cancer cutaneous lupus erythematosus gastric carcinoma lymphoplasmacytic lymphoma osteosarcoma prostate carcinoma astrocytic tumor chronic obstructive pulmonary disease dermatomyositis Hashimoto thyroiditis malignant mesothelioma ovarian cancer psoriasis autism spectrum disorder colorectal cancer endogenous depression lung carcinoma medulloblastoma primitive neuroectodermal tumor
A, B, C, D	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
E, F	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046
E, F	TPO	Parent Component: THR RESID: AA0037 , AA0038 PSI-MOD : O-phospho-L-serine MOD:00046 , 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.