Annotations: 5AIE

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5aiea1	Small proteins	RING/U-box	RING/U-box	RING finger domain, C3HC4	automated matches	BAKER'S YEAST (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d5aiea2	Artifacts	Tags	Tags	Tags	N-terminal Tags	BAKER'S YEAST (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d5aieb1	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	automated matches	BAKER'S YEAST (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d5aieb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	BAKER'S YEAST (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	RING finger domain C3HC4	8068303	4000374	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RING/U-box like	8068304	3000160	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	UBC-like	8034822	3000570	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF14570	e5aieA1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: PF14570	ECOD (1.6)
B	PF00179	e5aieB1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: PF00179	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF14570	RING/Ubox like zinc-binding domain (zf-RING_4)	RING/Ubox like zinc-binding domain	-	Domain
B	PF00179	Ubiquitin-conjugating enzyme (UQ_con)	Ubiquitin-conjugating enzyme	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cystein ...	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine [4, 5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4	RNA binding binding organic cyclic compound binding nucleic acid binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity cation binding RNA binding binding organic cyclic compound binding nucleic acid binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity cation binding ion binding metal ion binding small molecule binding	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process nucleobase-containing compound metabolic process organic substance biosynthetic process RNA catabolic process nuclear-transcribed mRNA catabolic process, deadenylation-independent decay mRNA catabolic process regulation of biological process cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process organic cyclic compound metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process regulation of metabolic process RNA decapping cellular biosynthetic process RNA metabolic process deadenylation-independent decapping of nuclear-transcribed mRNA negative regulation of cellular process mRNA methylguanosine-cap decapping negative regulation of macromolecule metabolic process regulation of biosynthetic process nuclear-transcribed mRNA catabolic process biological regulation regulation of macromolecule metabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound catabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process regulation of primary metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality positive regulation of nucleobase-containing compound metabolic process positive regulation of mRNA metabolic process nuclear-transcribed mRNA poly(A) tail shortening positive regulation of RNA metabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay positive regulation of biological process mRNA destabilization regulation of mRNA catabolic process RNA destabilization regulation of catabolic process positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process nuclear-transcribed mRNA catabolic process, no-go decay 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 protein polyubiquitination positive regulation of macromolecule biosynthetic process DNA-templated transcription transcription by RNA polymerase II regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II organic cyclic compound biosynthetic process regulation of DNA-templated transcription transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation positive regulation of cellular process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process DNA-templated transcription elongation positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process protein monoubiquitination	intracellular anatomical structure cytoplasm cellular anatomical entity CCR4-NOT complex protein-containing complex intracellular protein-containing complex intracellular organelle cytosolic ribosome organelle intracellular non-membrane-bounded organelle ribosome cytosol non-membrane-bounded organelle CCR4-NOT core complex intracellular anatomical structure cytoplasm cellular anatomical entity CCR4-NOT complex protein-containing complex intracellular protein-containing complex intracellular organelle cytosolic ribosome organelle intracellular non-membrane-bounded organelle ribosome cytosol non-membrane-bounded organelle CCR4-NOT core complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B	UBIQUITIN-CONJUGATING ENZYME E2 4	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ubiquitin conjugating enzyme activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity ubiquitin-protein transferase activity protein binding ubiquitin binding ubiquitin-like protein binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding protein-containing complex binding proteasome binding protein-macromolecule adaptor activity molecular adaptor activity	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process 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 organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process 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 protein polyubiquitination 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 proteasomal protein catabolic process mitochondria-associated ubiquitin-dependent protein catabolic process proteasome-mediated ubiquitin-dependent protein 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 process 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 ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway protein monoubiquitination ribosome-associated ubiquitin-dependent protein catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR003954	RNA recognition motif domain, eukaryote	Domain
A	IPR039515	NOT4, modified RING finger, HC subclass (C4C4-type)	Domain
A	IPR000504	RNA recognition motif domain	Domain
A	IPR000571	Zinc finger, CCCH-type	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A	IPR034261	CNOT4, RNA recognition motif	Domain
A	IPR039780	CCR4-NOT transcription complex subunit 4	Family
A	IPR001841	Zinc finger, RING-type	Domain
A	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
B	IPR000608	Ubiquitin-conjugating enzyme E2	Domain
B	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
B	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site

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 R01GM133198.