Annotations: 1ZC1

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	UFD1_N	e1zc1A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: UFD1_N	ECOD (1.6)
A	UFD1_C	e1zc1A2	A: a+b two layers	X: Cdc48 domain 2-like (From Topology)	H: Cdc48 domain 2-like (From Topology)	T: Cdc48 domain 2-like	F: UFD1_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.40.50	Mainly Beta	Beta Barrel	Barwin-like endoglucanases	Ubiquitin fusion degradation protein UFD1, N-terminal domain	CATH (4.3.0)
A	3.10.330.10	Alpha Beta	Roll	Vcp-like ATPase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03152	Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 1 (UFD1_N1)	Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 1	Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified [1]. UFD1 is a 40kD protein that is essential for vegetat ...	Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified [1]. UFD1 is a 40kD protein that is essential for vegetative cell viability [1]. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterised by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation [2]. UFD1 is composed of an N-terminal conserved region (UT3) and a C-terminal disordered region (UT6) which contains the binding sites for both Npl4 and Cdc48 [3, 4]. UFD1 N-terminal domain contains the binding site for ubiquitin [3, 4] and has a similar structure to p97. It is made of two subdomains [5]. This entry corresponds to the first subdomain of UFD1 UT3 which forms a double-psi beta barrel fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	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 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 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 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 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR042299	Ufd1-like, Nn domain	Homologous Superfamily
A	IPR004854	Ubiquitin fusion degradation protein Ufd1-like	Family

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.