Annotations: 6JWI

Yeast Npl4 in complex with Lys48-linked diubiquitin

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
D [auth G]	d6jwig_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth I]	d6jwii_	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)
C [auth E]	Ribonuc_L-PSP	e6jwiE1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
B [auth A]	Ribonuc_L-PSP	e6jwiA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
D [auth G]	Ribonuc_L-PSP	e6jwiG1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
A [auth I]	Ribonuc_L-PSP	e6jwiI1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A], C [auth E]	PF05020	NPL4 family, putative zinc binding region (zf-NPL4)	NPL4 family, putative zinc binding region	-	Family
B [auth A], C [auth E]	PF05021	NPL4 family (NPL4)	NPL4 family	-	Family
A [auth I], D [auth G]	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
B [auth A], C [auth E]	Nuclear protein localization protein 4	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 ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding	localization protein localization to organelle macromolecule localization protein localization to vacuole intracellular protein localization regulation of localization regulation of biological process regulation of protein localization positive regulation of protein localization to nucleus biological regulation positive regulation of biological process regulation of protein localization to nucleus protein localization to nucleus positive regulation of protein localization localization protein localization to organelle macromolecule localization protein localization to vacuole intracellular protein localization regulation of localization regulation of biological process regulation of protein localization positive regulation of protein localization to nucleus biological regulation positive regulation of biological process regulation of protein localization to nucleus protein localization to nucleus positive regulation of protein localization catabolic process primary metabolic process proteasomal protein catabolic process protein catabolic process mitochondria-associated ubiquitin-dependent protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process cellular component disassembly spindle disassembly microtubule cytoskeleton organization mitotic cell cycle mitotic spindle organization cellular component organization organelle organization mitotic cell cycle process organelle disassembly mitotic spindle disassembly microtubule-based process cell cycle cellular component organization or biogenesis cytoskeleton organization microtubule cytoskeleton organization involved in mitosis spindle organization cell cycle process RNA transport nitrogen compound transport transport nucleic acid transport mRNA transport establishment of localization establishment of RNA localization RNA localization nucleobase-containing compound transport nonfunctional rRNA decay RNA metabolic process rRNA catabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process rRNA metabolic process RNA catabolic process cellular response to stimulus response to stimulus ERAD pathway cellular response to stress response to chemical response to stress response to endoplasmic reticulum stress ribosome disassembly translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process translational elongation cytoplasmic translation cytoplasmic translational elongation rescue of stalled cytosolic ribosome cytoplasm protein quality control cellular response to misfolded protein response to misfolded protein cellular response to topologically incorrect protein cytoplasm protein quality control by the ubiquitin-proteasome system response to topologically incorrect protein protein quality control for misfolded or incompletely synthesized proteins DNA-templated DNA replication DNA replication DNA metabolic process DNA replication termination protein exit from endoplasmic reticulum cellular localization establishment of protein localization intercellular transport establishment of localization in cell endoplasmic reticulum to cytosol transport intracellular transport protein transport retrograde protein transport, ER to cytosol intracellular protein transport ribosome-associated ubiquitin-dependent protein catabolic process establishment of protein localization to plasma membrane vesicle-mediated transport endocytic recycling protein localization to cell periphery establishment of protein localization to membrane protein localization to plasma membrane localization within membrane protein localization to membrane endosomal transport vesicle-mediated transport to the plasma membrane endosome to plasma membrane protein transport	membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane membrane protein complex VCP-NPL4-UFD1 AAA ATPase complex intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure organelle nuclear outer membrane-endoplasmic reticulum membrane network membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane membrane protein complex VCP-NPL4-UFD1 AAA ATPase complex intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane nuclear membrane nucleus organelle envelope nuclear envelope RQC complex cytoplasmic ubiquitin ligase complex ubiquitin ligase complex transferase complex ER ubiquitin ligase complex catalytic complex Hrd1p ubiquitin ligase ERAD-L complex Hrd1p ubiquitin ligase complex intracellular protein-containing complex mitochondrial protein-containing complex mitochondrial membrane mitochondrion outer mitochondrial membrane protein complex organelle outer membrane bounding membrane of organelle Cdc48p-Npl4p-Vms1p AAA ATPase complex mitochondrial envelope mitochondrial outer membrane outer membrane Doa10p ubiquitin ligase complex perinuclear region of cytoplasm protein-DNA complex intracellular membraneless organelle chromosome membraneless organelle replication fork replisome
A [auth I], D [auth G]	Ubiqutin	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	translation at synapse primary metabolic process translation at presynapse translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process catabolic process modification-dependent macromolecule catabolic process translation at synapse primary metabolic process translation at presynapse translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process protein catabolic 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 cytoplasmic translation translation at postsynapse	cellular anatomical structure myelin sheath intracellular anatomical structure cytoplasm cytosol presynapse synapse cell junction membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure myelin sheath intracellular anatomical structure cytoplasm cytosol presynapse synapse cell junction membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle ribosome cytosolic ribosome protein-containing complex ribosomal subunit cytosolic large ribosomal subunit ribonucleoprotein complex large ribosomal subunit postsynapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A], C [auth E]	IPR007716	NPL4, zinc-binding putative	Domain
B [auth A], C [auth E]	IPR007717	Nuclear pore localisation protein NPL4, C-terminal	Domain
B [auth A], C [auth E]	IPR016563	Nuclear protein localization protein 4	Family
B [auth A], C [auth E]	IPR037518	MPN domain	Domain
B [auth A], C [auth E]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A [auth I], D [auth G]	IPR019954	Ubiquitin conserved site	Conserved Site
A [auth I], D [auth G]	IPR038587	Large ribosomal subunit protein eL40 superfamily	Homologous Superfamily
A [auth I], D [auth G]	IPR050158	Ubiquitin and ubiquitin-like	Family
A [auth I], D [auth G]	IPR000626	Ubiquitin-like domain	Domain
A [auth I], D [auth G]	IPR019956	Ubiquitin domain	Domain
A [auth I], D [auth G]	IPR001975	Large ribosomal subunit protein eL40 domain	Domain
A [auth I], D [auth G]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

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