Annotations: 6JWJ

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	UNK_F_TYPE	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: UNK_F_TYPE	ECOD (1.6)
A	UNK_F_TYPE	e6jwjA3	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)
A	UNK_F_TYPE	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: UNK_F_TYPE	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
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	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 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 modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process 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 response to nitrogen compound ERAD pathway cellular response to stress response to chemical response to stress response to endoplasmic reticulum stress cellular component disassembly ribosome disassembly rescue of stalled ribosome translation gene expression macromolecule biosynthetic process protein biosynthetic process cellular component organization organelle organization organelle disassembly biosynthetic process translational elongation cellular component organization or biogenesis 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 nitrogen compound transport transport establishment of localization in cell endoplasmic reticulum to cytosol transport intracellular transport 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 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 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 intracellular membraneless organelle chromosome membraneless organelle replication fork replisome Hrd1p ubiquitin ligase ERAD-L complex Hrd1p ubiquitin ligase complex nucleus
A	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 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 modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein 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 response to nitrogen compound ERAD pathway cellular response to stress response to chemical response to stress response to endoplasmic reticulum stress ribosome disassembly rescue of stalled ribosome translation gene expression macromolecule biosynthetic process protein biosynthetic process biosynthetic process translational elongation 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 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C]	IPR042299	Ufd1-like, Nn domain	Homologous Superfamily
B [auth C]	IPR055417	Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 1	Domain
B [auth C]	IPR055418	Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 2	Domain
B [auth C]	IPR004854	Ubiquitin fusion degradation protein Ufd1-like	Family
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

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.