Annotations: 6JWI

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth I]	ubiquitin_1	e6jwiI1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
D [auth G]	ubiquitin_1	e6jwiG1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
B [auth A]	UNK_F_TYPE	e6jwiA2	A: alpha arrays	X: C-terminal domain of Npl4 (From Topology)	H: C-terminal domain of Npl4 (From Topology)	T: C-terminal domain of Npl4	F: UNK_F_TYPE	ECOD (1.6)
B [auth A]	UNK_F_TYPE	e6jwiA3	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: UNK_F_TYPE	ECOD (1.6)
B [auth A]	UNK_F_TYPE	e6jwiA4	A: few secondary structure elements	X: Npl4 zinc binding domain (From Topology)	H: Npl4 zinc binding domain (From Topology)	T: Npl4 zinc binding domain	F: UNK_F_TYPE	ECOD (1.6)
C [auth E]	UNK_F_TYPE	e6jwiE1	A: alpha arrays	X: C-terminal domain of Npl4 (From Topology)	H: C-terminal domain of Npl4 (From Topology)	T: C-terminal domain of Npl4	F: UNK_F_TYPE	ECOD (1.6)
C [auth E]	UNK_F_TYPE	e6jwiE2	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: UNK_F_TYPE	ECOD (1.6)
C [auth E]	UNK_F_TYPE	e6jwiE3	A: few secondary structure elements	X: Npl4 zinc binding domain (From Topology)	H: Npl4 zinc binding domain (From Topology)	T: Npl4 zinc binding domain	F: UNK_F_TYPE	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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	organonitrogen compound metabolic process translation at synapse cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process translation at presynapse translation gene expression macromolecule biosynthetic process organic substance metabolic process biosynthetic process organic substance biosynthetic process metabolic process organonitrogen compound metabolic process translation at synapse cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process translation at presynapse translation gene expression macromolecule biosynthetic process organic substance metabolic process biosynthetic process organic substance biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic 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 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	myelin sheath cellular anatomical entity intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane presynapse synapse cell junction membrane-bounded organelle nucleus membrane-enclosed lumen myelin sheath cellular anatomical entity intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane 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 intracellular non-membrane-bounded organelle ribosome non-membrane-bounded organelle cytosolic ribosome protein-containing complex ribosomal subunit cytosolic large ribosomal subunit ribonucleoprotein complex large ribosomal subunit cytosolic small ribosomal subunit small ribosomal subunit postsynapse endoplasmic reticulum endomembrane system
B [auth A], C [auth E]	Nuclear protein localization protein 4	protein binding binding ubiquitin binding ubiquitin-like protein binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding	protein localization localization cellular localization protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to vacuole cellular process regulation of localization regulation of biological process regulation of cellular process regulation of protein localization positive regulation of protein localization to nucleus biological regulation protein localization localization cellular localization protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to vacuole cellular process regulation of localization regulation of biological process regulation of cellular 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 regulation of cellular localization positive regulation of protein localization positive regulation of cellular process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein 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 organic substance metabolic 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 organic substance catabolic 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 organic substance 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 organic cyclic compound catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process ncRNA metabolic process nucleic acid catabolic process rRNA metabolic process RNA catabolic process cellular biosynthetic process rescue of stalled ribosome organonitrogen compound biosynthetic process organic substance biosynthetic process ribosome disassembly cellular metabolic process translation gene expression macromolecule biosynthetic process biosynthetic process translational elongation cellular response to stimulus response to organic substance cytoplasm protein quality control response to stimulus cellular response to misfolded protein response to misfolded protein cellular response to stress response to stress cellular response to organic substance cellular response to topologically incorrect protein cytoplasm protein quality control by the ubiquitin-proteasome system cellular response to chemical stimulus response to chemical response to topologically incorrect protein protein quality control for misfolded or incompletely synthesized proteins DNA-templated DNA replication DNA metabolic process DNA replication termination DNA replication protein exit from endoplasmic reticulum establishment of protein localization ERAD pathway establishment of localization in cell response to endoplasmic reticulum stress endoplasmic reticulum to cytosol transport response to organonitrogen compound intracellular transport response to nitrogen compound protein transport retrograde protein transport, ER to cytosol intracellular protein transport ribosome-associated ubiquitin-dependent protein catabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane membrane protein complex VCP-NPL4-UFD1 AAA ATPase complex cellular anatomical entity intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle 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 cellular anatomical entity intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle 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 chromosome intracellular non-membrane-bounded organelle replication fork replisome non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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]	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
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

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.