3I3T

Crystal structure of covalent ubiquitin-USP21 complex

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3i3ta_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth C]	d3i3tc_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth E]	d3i3te_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth G]	d3i3tg_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth B]	d3i3tb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth D]	d3i3td_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G [auth F]	d3i3tf_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d3i3th_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Cysteine proteinases	8067279	3001808	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Cysteine proteinases	8067279	3001808	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	Cysteine proteinases	8067279	3001808	SCOP2B (2022-06-29)
D [auth G]	SCOP2B Superfamily	Cysteine proteinases	8067279	3001808	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
G [auth F]	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ubiquitin-like	8066187	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	UCH	e3i3tA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: UCH	ECOD (1.6)
B [auth C]	UCH	e3i3tC1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: UCH	ECOD (1.6)
C [auth E]	UCH	e3i3tE1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: UCH	ECOD (1.6)
D [auth G]	UCH	e3i3tG1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: UCH	ECOD (1.6)
E [auth B]	ubiquitin_1	e3i3tB1	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	e3i3tD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
G [auth F]	ubiquitin_1	e3i3tF1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
H	ubiquitin_1	e3i3tH1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
B [auth C]	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
C [auth E]	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
D [auth G]	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
E [auth B]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
F [auth D]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
G [auth F]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
H	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, B [auth C], C [auth E], D [auth G]	PF00443	Ubiquitin carboxyl-terminal hydrolase (UCH)	Ubiquitin carboxyl-terminal hydrolase	-	Family
E [auth B], F [auth D], G [auth F], H	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, B [auth C], C [auth E], D [auth G]	Ubiquitin carboxyl-terminal hydrolase 21	cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity deNEDDylase activity transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity deNEDDylase activity transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity cation binding ion binding binding metal ion binding small molecule binding	regulation of cellular process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription transcription by RNA polymerase II chromatin organization organic substance biosynthetic process positive regulation of macromolecule metabolic process transcription initiation at RNA polymerase II promoter regulation of biological process cellular metabolic process regulation of cellular metabolic process regulation of cellular process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription transcription by RNA polymerase II chromatin organization organic substance biosynthetic process positive regulation of macromolecule metabolic process transcription initiation at RNA polymerase II promoter regulation of biological process cellular metabolic process regulation of cellular metabolic process primary metabolic process regulation of gene expression organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process protein-DNA complex organization cellular component organization RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process positive regulation of biosynthetic process chromatin remodeling cellular component organization or biogenesis positive regulation of cellular process regulation of biosynthetic process protein-containing complex organization epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of cellular biosynthetic process positive regulation of gene expression cellular process positive regulation of cellular biosynthetic process organonitrogen compound metabolic process proteolysis protein metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
E [auth B], F [auth D], G [auth F], H	Ubiquitin	structural molecule activity structural constituent of ribosome protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	organic substance metabolic process organonitrogen compound metabolic process macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process organic substance metabolic process organonitrogen compound metabolic process macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis organic substance catabolic process protein ubiquitination post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process translation gene expression macromolecule biosynthetic process biosynthetic process organic substance biosynthetic process cytoplasmic translation cellular process	membrane-bounded organelle organelle cellular anatomical entity vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery membrane-bounded organelle organelle cellular anatomical entity vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane endocytic vesicle vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome cytosolic ribosome intracellular non-membrane-bounded organelle ribosome non-membrane-bounded organelle endosome membrane endosome mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane protein-containing complex ribosomal subunit cytosolic large ribosomal subunit ribonucleoprotein complex large ribosomal subunit cytosolic small ribosomal subunit small ribosomal subunit

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth E], D [auth G]	IPR028889	Ubiquitin specific protease domain	Domain
A, B [auth C], C [auth E], D [auth G]	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
A, B [auth C], C [auth E], D [auth G]	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
A, B [auth C], C [auth E], D [auth G]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
E [auth B], F [auth D], G [auth F], H	IPR019954	Ubiquitin conserved site	Conserved Site
E [auth B], F [auth D], G [auth F], H	IPR038587	Large ribosomal subunit protein eL40 superfamily	Homologous Superfamily
E [auth B], F [auth D], G [auth F], H	IPR000626	Ubiquitin-like domain	Domain
E [auth B], F [auth D], G [auth F], H	IPR019956	Ubiquitin domain	Domain
E [auth B], F [auth D], G [auth F], H	IPR001975	Large ribosomal subunit protein eL40 domain	Domain
E [auth B], F [auth D], G [auth F], H	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B [auth C], C [auth E], D [auth G]	Pharos: Q9UK80	allergic rhinitis ovarian cancer lung cancer malignant mesothelioma
E [auth B], F [auth D], G [auth F], H	Pharos: P62987	attention deficit hyperactivity disorder, inattentive type heart disease dental caries lung cancer gastroesophageal reflux disease plasma cell myeloma

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.