Annotations: 6JWJ

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF05021	e6jwjA4	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: PF05021	ECOD (1.6)
A	PF05021	e6jwjA3	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: PF05021	ECOD (1.6)
A	PF05020	e6jwjA1	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: PF05020	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF05020	NPL4 family, putative zinc binding region (zf-NPL4)	NPL4 family, putative zinc binding region	-	Family
A	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	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
B [auth C]	Peptide from Ubiquitin fusion degradation protein 1	polyubiquitin modification-dependent protein binding protein binding binding modification-dependent protein binding ubiquitin binding ubiquitin-like protein 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 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 cellular component organization organelle disassembly organic substance biosynthetic process cellular component organization or biogenesis cellular component disassembly ribosome disassembly cellular metabolic process translation gene expression macromolecule biosynthetic process organelle organization 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 nitrogen compound transport transport ERAD pathway establishment of localization in cell response to endoplasmic reticulum stress endoplasmic reticulum to cytosol transport response to organonitrogen compound organic substance transport intracellular transport response to nitrogen compound establishment of localization 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 cytoplasmic ubiquitin ligase complex ubiquitin ligase complex transferase complex ER ubiquitin ligase complex catalytic complex Doa10p ubiquitin ligase complex intracellular protein-containing complex cytosol RQC complex protein-DNA complex chromosome intracellular non-membrane-bounded organelle replication fork replisome non-membrane-bounded organelle Hrd1p ubiquitin ligase ERAD-L complex Hrd1p ubiquitin ligase complex nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR007716	NPL4, zinc-binding putative	Domain
A	IPR007717	Nuclear pore localisation protein NPL4, C-terminal	Domain
A	IPR016563	Nuclear protein localization protein 4	Family
A	IPR037518	MPN domain	Domain
A	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B [auth C]	IPR042299	Ufd1-like, Nn domain	Homologous Superfamily
B [auth C]	IPR004854	Ubiquitin fusion degradation protein Ufd1-like	Family

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.