4XKH

CRYSTAL STRUCTURE OF THE AIRAPL TANDEM UIMS IN COMPLEX WITH A LYS48-LINKED TRI-UBIQUITIN

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	d4xkha_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Bovine (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
C [auth F]	d4xkhf_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Bovine (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
D [auth B]	d4xkhb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Bovine (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
F [auth D]	d4xkhd_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Bovine (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
G	d4xkhg_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Bovine (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
I	d4xkhi_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Bovine (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
C [auth F]	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	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	ubiquitin	e4xkhA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin	ECOD (1.6)
C [auth F]	ubiquitin_1	e4xkhF1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
D [auth B]	ubiquitin_1	e4xkhB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
F [auth D]	ubiquitin_1	e4xkhD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
G	ubiquitin_1	e4xkhG1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
I	ubiquitin_1	e4xkhI1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
B [auth E]	UNK_F_TYPE	e4xkhE1	A: extended segments	X: UIM domain (From Topology)	H: UIM domain (From Topology)	T: UIM domain	F: UNK_F_TYPE	ECOD (1.6)
E [auth C]	UNK_F_TYPE	e4xkhC1	A: extended segments	X: UIM domain (From Topology)	H: UIM domain (From Topology)	T: UIM domain	F: UNK_F_TYPE	ECOD (1.6)
H	UNK_F_TYPE	e4xkhH1	A: extended segments	X: UIM domain (From Topology)	H: UIM domain (From Topology)	T: UIM domain	F: UNK_F_TYPE	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth F], D [auth B], F [auth D], G, A, C [auth F], D [auth B], F [auth D], G, I	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, C [auth F], D [auth B], F [auth D], G, A, C [auth F], D [auth B], F [auth D], G, I	Polyubiquitin-C	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process protein ubiquitination macromolecule modification post-translational protein modification catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic 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	membrane-bounded organelle intracellular anatomical structure mitochondrial membrane mitochondrion membrane organelle outer membrane cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle organelle envelope bounding membrane of organelle organelle mitochondrial envelope mitochondrial outer membrane membrane-bounded organelle intracellular anatomical structure mitochondrial membrane mitochondrion membrane organelle outer membrane cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle organelle envelope bounding membrane of organelle organelle mitochondrial envelope mitochondrial outer membrane outer membrane cytoplasm organelle membrane nucleus
B [auth E], E [auth C], H	AN1-type zinc finger protein 2B	polyubiquitin modification-dependent protein binding protein binding binding K48-linked polyubiquitin modification-dependent protein binding modification-dependent protein binding ubiquitin binding ubiquitin-like protein binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation regulation of signal transduction insulin-like growth factor receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway cell communication regulation of response to stimulus regulation of insulin-like growth factor receptor signaling pathway cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation regulation of signal transduction insulin-like growth factor receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway cell communication regulation of response to stimulus regulation of insulin-like growth factor receptor signaling pathway regulation of cell communication cellular process signal transduction enzyme-linked receptor protein signaling pathway catabolic process proteolysis involved in protein catabolic process primary metabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process protein metabolic process macromolecule metabolic process protein localization establishment of protein localization cellular localization protein targeting establishment of localization localization establishment of protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to organelle establishment of protein localization to endoplasmic reticulum protein localization to endoplasmic reticulum protein targeting to ER nitrogen compound transport transport SRP-dependent cotranslational protein targeting to membrane protein transmembrane transport establishment of localization in cell cotranslational protein targeting to membrane establishment of protein localization to membrane intracellular protein transmembrane transport intracellular transport localization within membrane protein localization to membrane protein targeting to membrane transmembrane transport protein transport SRP-dependent cotranslational protein targeting to membrane, translocation intracellular protein transport	protein-containing complex catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex membrane cellular anatomical entity intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle endoplasmic reticulum protein-containing complex catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex membrane cellular anatomical entity intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle endoplasmic reticulum intracellular membrane-bounded organelle endomembrane system organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth F], D [auth B], F [auth D], G, A, C [auth F], D [auth B], F [auth D], G, I	IPR019956	Ubiquitin domain	Domain
A, C [auth F], D [auth B], F [auth D], G, A, C [auth F], D [auth B], F [auth D], G, I	IPR019954	Ubiquitin conserved site	Conserved Site
A, C [auth F], D [auth B], F [auth D], G, A, C [auth F], D [auth B], F [auth D], G, I	IPR050158	Ubiquitin and ubiquitin-like	Family
A, C [auth F], D [auth B], F [auth D], G, A, C [auth F], D [auth B], F [auth D], G, I	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, C [auth F], D [auth B], F [auth D], G, A, C [auth F], D [auth B], F [auth D], G, I	IPR000626	Ubiquitin-like domain	Domain
B [auth E], E [auth C], H	IPR000058	Zinc finger, AN1-type	Domain
B [auth E], E [auth C], H	IPR035896	AN1-like Zinc finger	Homologous Superfamily
B [auth E], E [auth C], H	IPR003903	Ubiquitin interacting motif	Conserved Site

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.