Annotations: 3A1Q

Crystal structure of the mouse RAP80 UIMs in complex with Lys63-linked di-ubiquitin

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3a1qa_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d3a1qd_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d3a1qb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d3a1qe_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	YgbB	e3a1qA1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
D	YgbB	e3a1qD1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
B	YgbB	e3a1qB1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
E	YgbB	e3a1qE1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v295)
C	ColA_N	e3a1qC01	A: alpha arrays	X: Colicin-A N-terminal domain	H: Colicin-A N-terminal domain	T: Colicin-A N-terminal domain	F: ColA_N	ECOD (v295)
F	Med6	e3a1qF1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Med6	ECOD (v295)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
E	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain
B, E	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain
C, F	PF18282	RAP80 N-terminal ubiquitin interaction motif (RAP80_UIM)	RAP80 N-terminal ubiquitin interaction motif	This is the N-terminal domain found in RAP80 protein present in Homo sapiens. RAP80 is fundamental for protein recruitment in the DNA damage response. The N-terminal domain is a ubiquitin-interacting motif (UIM). RAP80 is involved in multivalent rec ...	This is the N-terminal domain found in RAP80 protein present in Homo sapiens. RAP80 is fundamental for protein recruitment in the DNA damage response. The N-terminal domain is a ubiquitin-interacting motif (UIM). RAP80 is involved in multivalent recognition of polyUb chains through N-terminal domain [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D	Ubiquitin	protein tag activity molecular tag activity structural molecule activity structural constituent of ribosome	catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	cellular anatomical structure myelin sheath intracellular organelle intracellular anatomical structure cytosolic ribosome organelle membraneless organelle intracellular membraneless organelle ribosome cytoplasm cytosol membrane-bounded organelle mitochondrial membrane mitochondrion cellular anatomical structure myelin sheath intracellular organelle intracellular anatomical structure cytosolic ribosome organelle membraneless organelle intracellular membraneless organelle ribosome cytoplasm cytosol membrane-bounded organelle mitochondrial membrane mitochondrion membrane organelle outer membrane intracellular membrane-bounded organelle organelle envelope bounding membrane of organelle mitochondrial envelope mitochondrial outer membrane outer membrane organelle membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B, E	Ubiquitin	protein tag activity molecular tag activity structural molecule activity structural constituent of ribosome	catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	cellular anatomical structure myelin sheath intracellular organelle intracellular anatomical structure cytosolic ribosome organelle membraneless organelle intracellular membraneless organelle ribosome cytoplasm cytosol membrane-bounded organelle mitochondrial membrane mitochondrion cellular anatomical structure myelin sheath intracellular organelle intracellular anatomical structure cytosolic ribosome organelle membraneless organelle intracellular membraneless organelle ribosome cytoplasm cytosol membrane-bounded organelle mitochondrial membrane mitochondrion membrane organelle outer membrane intracellular membrane-bounded organelle organelle envelope bounding membrane of organelle mitochondrial envelope mitochondrial outer membrane outer membrane organelle membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
C, F	Ubiquitin interaction motif-containing protein 1	DNA binding binding nucleic acid binding protein binding histone binding transcription factor binding nuclear retinoic acid receptor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding nuclear retinoid X receptor binding DNA-binding transcription factor binding ubiquitin-modified protein reader activity ubiquitin-modified histone reader activity histone reader activity DNA binding binding nucleic acid binding protein binding histone binding transcription factor binding nuclear retinoic acid receptor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding nuclear retinoid X receptor binding DNA-binding transcription factor binding ubiquitin-modified protein reader activity ubiquitin-modified histone reader activity histone reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity ubiquitin-like protein reader activity molecular adaptor activity polyubiquitin modification-dependent protein binding modification-dependent protein binding K63-linked polyubiquitin modification-dependent protein binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process response to ionizing radiation response to stimulus response to radiation response to abiotic stimulus cellular response to stimulus regulation of cell cycle phase transition DNA damage checkpoint signaling signaling G2/M transition of mitotic cell cycle mitotic G2 DNA damage checkpoint signaling negative regulation of cell cycle cell cycle phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle mitotic G2/M transition checkpoint cell communication regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling cellular response to stress response to stress mitotic DNA damage checkpoint signaling negative regulation of cell cycle phase transition signal transduction cell cycle regulation of cell cycle cell cycle process cell cycle G2/M phase transition negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process 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 DNA damage response negative regulation of cell cycle G2/M phase transition signal transduction in response to DNA damage negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition DNA repair-dependent chromatin remodeling cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis double-strand break repair DNA metabolic process DNA repair regulation of cellular response to stress regulation of response to stress regulation of DNA repair regulation of response to stimulus regulation of DNA metabolic process positive regulation of biological process positive regulation of response to stimulus positive regulation of metabolic process positive regulation of DNA repair positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of DNA metabolic process	intracellular organelle site of double-strand break cellular anatomical structure intracellular anatomical structure organelle membraneless organelle site of DNA damage intracellular membraneless organelle chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle site of double-strand break cellular anatomical structure intracellular anatomical structure organelle membraneless organelle site of DNA damage intracellular membraneless organelle chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear body nucleoplasm organelle lumen nuclear lumen protein-containing complex nuclear protein-containing complex BRCA1-A complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D	IPR019954	Ubiquitin conserved site	Conserved Site
A, D	IPR000626	Ubiquitin-like domain	Domain
A, D	IPR019956	Ubiquitin domain	Domain
A, D	IPR050158	Ubiquitin and ubiquitin-like	Family
A, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B, E	IPR019954	Ubiquitin conserved site	Conserved Site
B, E	IPR000626	Ubiquitin-like domain	Domain
B, E	IPR019956	Ubiquitin domain	Domain
B, E	IPR050158	Ubiquitin and ubiquitin-like	Family
B, E	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
C, F	IPR040714	RAP80, N-terminal	Domain
C, F	IPR003903	Ubiquitin interacting motif	Conserved Site
C, F	IPR006642	Rad18, zinc finger UBZ4-type	Domain
C, F	IPR038868	BRCA1-A complex subunit RAP80	Family

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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.