6J0Y | pdb_00006j0y

Crystal Structure of Yeast Rtt107 and Slx4

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth B]	PTCB-BRCT	e6j0yB1	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 [auth B]	UNK_F_TYPE	e6j0yB4	A: a/b three-layered sandwiches	X: BRCT domain (From Topology)	H: BRCT domain (From Topology)	T: BRCT domain	F: UNK_F_TYPE	ECOD (1.6)
A	PTCB-BRCT	e6j0yA1	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	UNK_F_TYPE	e6j0yA4	A: a/b three-layered sandwiches	X: BRCT domain (From Topology)	H: BRCT domain (From Topology)	T: BRCT domain	F: UNK_F_TYPE	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B]	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
B [auth C], D	Peptide from Structure-specific endonuclease subunit SLX4	5'-flap endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity flap endonuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of cellular process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of cellular process sexual reproduction homologous recombination regulation of reproductive process reproductive process meiotic DNA double-strand break formation involved in reciprocal meiotic recombination meiotic cell cycle process regulation of primary metabolic process cellular component organization regulation of meiotic DNA double-strand break formation meiosis I meiotic nuclear division regulation of nucleobase-containing compound metabolic process cell cycle cellular component organization or biogenesis regulation of cell cycle reciprocal homologous recombination regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination cell cycle process regulation of biological process regulation of cell cycle process meiotic cell cycle DNA recombination organelle fission biological regulation regulation of macromolecule metabolic process meiotic DNA double-strand break formation reciprocal meiotic recombination nuclear division organelle organization meiosis I cell cycle process regulation of metabolic process regulation of DNA metabolic process DNA double-strand break processing DNA repair double-strand break repair regulation of DNA double-strand break processing regulation of cellular component organization DNA-templated DNA replication maintenance of fidelity negative regulation of biological process maintenance of DNA repeat elements negative regulation of DNA-templated DNA replication regulation of replication fork arrest at rDNA repeats negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process replication fork arrest at rDNA repeats DNA-templated DNA replication negative regulation of DNA replication negative regulation of metabolic process chromosome organization regulation of chromosome organization regulation of organelle organization maintenance of rDNA regulation of DNA-templated DNA replication replication fork arrest negative regulation of DNA metabolic process regulation of DNA replication interstrand cross-link repair double-strand break repair via single-strand annealing double-strand break repair via single-strand annealing, removal of nonhomologous ends removal of nonhomologous ends DNA damage checkpoint signaling regulation of cell cycle phase transition signaling regulation of cellular response to stress negative regulation of cell cycle cell cycle phase transition regulation of signal transduction intracellular signal transduction cell communication regulation of cell cycle checkpoint regulation of intracellular signal transduction regulation of response to stress negative regulation of cell cycle phase transition signal transduction regulation of signaling DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling regulation of response to stimulus signal transduction in response to DNA damage regulation of cell communication regulation of DNA damage checkpoint double-strand break repair via break-induced replication recombinational repair double-strand break repair via homologous recombination	protein-containing complex catalytic complex intracellular protein-containing complex endonuclease complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome intracellular membraneless organelle chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle protein-containing complex catalytic complex intracellular protein-containing complex endonuclease complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome intracellular membraneless organelle chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen nuclear protein-containing complex Slx1-Slx4 complex cytoplasm
A, C [auth B]	Regulator of Ty1 transposition protein 107	chromatin binding binding	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization regulation of cellular process protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization regulation of cellular process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process retrotransposition regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression transposition macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process transposable element silencing regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process localization DNA double-strand break attachment to nuclear envelope chromosome localization organelle localization chromosome attachment to the nuclear envelope cell cycle cell cycle process cellular response to stimulus response to stimulus DNA double-strand break processing regulation of primary metabolic process nucleobase-containing compound metabolic process cellular response to stress response to stress regulation of nucleobase-containing compound metabolic process DNA repair double-strand break repair regulation of DNA double-strand break processing primary metabolic process DNA metabolic process nucleic acid metabolic process DNA damage response regulation of DNA metabolic process DNA damage checkpoint signaling regulation of cell cycle phase transition signaling regulation of cellular response to stress negative regulation of cell cycle cell cycle phase transition regulation of signal transduction intracellular signal transduction cell communication regulation of cell cycle checkpoint regulation of intracellular signal transduction regulation of response to stress negative regulation of cell cycle phase transition signal transduction regulation of cell cycle regulation of signaling regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling regulation of response to stimulus signal transduction in response to DNA damage regulation of cell communication regulation of DNA damage checkpoint	cell periphery cellular anatomical structure Cul8-RING ubiquitin ligase complex cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus cell periphery cellular anatomical structure Cul8-RING ubiquitin ligase complex cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C], D	IPR027784	Structure-specific endonuclease subunit Slx4, ascomycetes	Family
B [auth C], D	IPR018574	Structure-specific endonuclease subunit Slx4	Family
A, C [auth B]	IPR053036	Cell Cycle and DNA Repair Regulator	Family
A, C [auth B]	IPR031906	Regulator of Ty1 transposition protein 107, BRCT domain	Domain
A, C [auth B]	IPR001357	BRCT domain	Domain
A, C [auth B]	IPR036420	BRCT domain superfamily	Homologous Superfamily

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.