3A9J

Crystal structure of the mouse TAB2-NZF in complex with Lys63-linked di-ubiquitin

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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	d3a9ja_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d3a9jb_	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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2 Family	Ran binding protein zinc finger-like	8081680	4000343	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Ran binding protein zinc finger-like	8081681	3000133	SCOP2 (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	PF00240	e3a9jA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
B	PF00240	e3a9jB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
C	PF00641	e3a9jC1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PF00641	ECOD (1.6)

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)
B	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	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	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ubiquitin	protein binding binding enzyme binding protease binding protein tag activity molecular tag activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organic substance 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	myelin sheath cellular anatomical entity intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle mitochondrial membrane mitochondrion membrane organelle outer membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope bounding membrane of organelle myelin sheath cellular anatomical entity intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle mitochondrial membrane mitochondrion membrane organelle outer membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope bounding membrane of organelle organelle mitochondrial envelope mitochondrial outer membrane outer membrane organelle membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B	Ubiquitin	protein binding binding enzyme binding protease binding protein tag activity molecular tag activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organic substance 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	myelin sheath cellular anatomical entity intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle mitochondrial membrane mitochondrion membrane organelle outer membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope bounding membrane of organelle myelin sheath cellular anatomical entity intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle mitochondrial membrane mitochondrion membrane organelle outer membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope bounding membrane of organelle organelle mitochondrial envelope mitochondrial outer membrane outer membrane organelle membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
C	Mitogen-activated protein kinase kinase kinase 7-interacting protein 2	molecular adaptor activity protein binding binding ubiquitin binding ubiquitin-like protein binding 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	developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction cellular process positive regulation of signaling defense response response to stress inflammatory response positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process phosphorus metabolic process protein modification process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of protein metabolic process regulation of cellular metabolic process primary metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity macromolecule modification regulation of phosphorus metabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of cellular metabolic process positive regulation of molecular function positive regulation of protein modification process organic substance metabolic process protein metabolic process positive regulation of protein kinase activity organonitrogen compound metabolic process positive regulation of transferase activity positive regulation of catalytic activity regulation of protein kinase activity regulation of macromolecule metabolic process regulation of phosphorylation biological process involved in interspecies interaction between organisms response to other organism response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to bacterium response to external biotic stimulus response to organic substance response to lipid response to oxygen-containing compound response to lipopolysaccharide response to chemical response to molecule of bacterial origin non-canonical NF-kappaB signal transduction	vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cytoplasm vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cytoplasm organelle membrane lysosome cytosol endosome membrane endosome intracellular vesicle endomembrane system cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle vesicle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR019954	Ubiquitin conserved site	Conserved Site
A	IPR000626	Ubiquitin-like domain	Domain
A	IPR019956	Ubiquitin domain	Domain
A	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B	IPR019954	Ubiquitin conserved site	Conserved Site
B	IPR000626	Ubiquitin-like domain	Domain
B	IPR019956	Ubiquitin domain	Domain
B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
C	IPR041911	TAB2/3, CUE domain	Domain
C	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
C	IPR001876	Zinc finger, RanBP2-type	Domain
C	IPR003892	Ubiquitin system component CUE	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.