2QIY

yeast Deubiquitinase Ubp3 and Bre5 cofactor 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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2qiya_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	NTF2-like	UBP3-associated protein BRE5	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C [auth B]	d2qiyb_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	NTF2-like	UBP3-associated protein BRE5	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	NTF2-like	8023638	4001021	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	NTF2-like	8036018	3000472	SCOP2 (2022-06-29)
C [auth B]	SCOP2B Superfamily	NTF2-like	8036018	3000472	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	NTF2	e2qiyA1	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: NTF2	ECOD (1.6)
C [auth B]	NTF2	e2qiyB1	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: NTF2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.450.50	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
C [auth B]	3.10.450.50	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B]	PF02136	Nuclear transport factor 2 (NTF2) domain (NTF2)	Nuclear transport factor 2 (NTF2) domain	This family includes the NTF2-like Delta-5-3-ketosteroid isomerase proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B]	UBP3-associated protein BRE5	RNA binding binding nucleic acid binding mRNA binding identical protein binding protein binding	catabolic process regulation of cellular process macroautophagy autophagy negative regulation of biological process regulation of autophagy mitophagy negative regulation of cellular process regulation of autophagy of mitochondrion process utilizing autophagic mechanism negative regulation of catabolic process regulation of biological process negative regulation of metabolic process negative regulation of autophagy of mitochondrion catabolic process regulation of cellular process macroautophagy autophagy negative regulation of biological process regulation of autophagy mitophagy negative regulation of cellular process regulation of autophagy of mitochondrion process utilizing autophagic mechanism negative regulation of catabolic process regulation of biological process negative regulation of metabolic process negative regulation of autophagy of mitochondrion biological regulation regulation of mitophagy regulation of catabolic process negative regulation of mitophagy negative regulation of macroautophagy regulation of macroautophagy negative regulation of autophagy cellular process metabolic process regulation of metabolic process autophagy of mitochondrion regulation of localization cellular localization regulation of ER to Golgi vesicle-mediated transport transport regulation of transport intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport localization regulation of cellular localization establishment of localization in cell Golgi vesicle transport regulation of intracellular transport cellular component biogenesis cellular component organization organelle organization cellular component assembly stress granule assembly organelle assembly membraneless organelle assembly cellular component organization or biogenesis protein deubiquitination primary metabolic process protein modification by small protein removal macromolecule modification protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal maintenance of protein location protein localization protein localization to Golgi apparatus maintenance of location maintenance of location in cell maintenance of protein location in cell cellular macromolecule localization macromolecule localization protein localization to organelle protein retention in Golgi apparatus regulation of retrograde vesicle-mediated transport, Golgi to ER retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum ribophagy	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex cytoplasmic stress granule membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex cytoplasmic stress granule cytosol P-body protein-containing complex catalytic complex peptidase complex Ubp3-Bre5 deubiquitination complex
B [auth C], D	Ubiquitin carboxyl-terminal hydrolase 3	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 RNA binding binding nucleic acid binding mRNA binding	catabolic process regulation of cellular process macroautophagy autophagy negative regulation of biological process regulation of autophagy mitophagy negative regulation of cellular process regulation of autophagy of mitochondrion process utilizing autophagic mechanism negative regulation of catabolic process regulation of biological process negative regulation of metabolic process negative regulation of autophagy of mitochondrion catabolic process regulation of cellular process macroautophagy autophagy negative regulation of biological process regulation of autophagy mitophagy negative regulation of cellular process regulation of autophagy of mitochondrion process utilizing autophagic mechanism negative regulation of catabolic process regulation of biological process negative regulation of metabolic process negative regulation of autophagy of mitochondrion biological regulation regulation of mitophagy regulation of catabolic process negative regulation of mitophagy negative regulation of macroautophagy regulation of macroautophagy negative regulation of autophagy cellular process metabolic process regulation of metabolic process autophagy of mitochondrion regulation of protein stability regulation of biological quality regulation of localization cellular localization regulation of ER to Golgi vesicle-mediated transport transport regulation of transport intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport localization regulation of cellular localization establishment of localization in cell Golgi vesicle transport regulation of intracellular transport cellular component biogenesis cellular component organization organelle organization cellular component assembly stress granule assembly organelle assembly membraneless organelle assembly cellular component organization or biogenesis protein deubiquitination primary metabolic process protein modification by small protein removal macromolecule modification protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal maintenance of protein location protein localization protein localization to Golgi apparatus maintenance of location maintenance of location in cell maintenance of protein location in cell cellular macromolecule localization macromolecule localization protein localization to organelle protein retention in Golgi apparatus regulation of retrograde vesicle-mediated transport, Golgi to ER retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum proteolysis response to osmotic stress response to stimulus regulation of response to stimulus regulation of response to stress response to stress response to abiotic stimulus regulation of response to osmotic stress ribophagy	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol protein-containing complex catalytic complex peptidase complex Ubp3-Bre5 deubiquitination complex nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B]	IPR032710	NTF2-like domain superfamily	Homologous Superfamily
A, C [auth B]	IPR000504	RNA recognition motif domain	Domain
A, C [auth B]	IPR018222	Nuclear transport factor 2, eukaryote	Domain
A, C [auth B]	IPR002075	Nuclear transport factor 2 domain	Domain
A, C [auth B]	IPR039539	Ras GTPase-activating protein-binding protein	Family
B [auth C], D	IPR028889	Ubiquitin specific protease domain	Domain
B [auth C], D	IPR050164	Ubiquitin carboxyl-terminal hydrolases	Family
B [auth C], D	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
B [auth C], D	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
B [auth C], D	IPR038765	Papain-like cysteine peptidase 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.