9KHT | pdb_00009kht

cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked triUb (dimeric conformation)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L [auth b]	SCOP2B Superfamily	UBC-like	8034822	3000570	SCOP2B (2022-06-29)
J [auth B]	SCOP2B Superfamily	UBC-like	8034822	3000570	SCOP2B (2022-06-29)
K [auth a]	SCOP2B Superfamily	RING/U-box like	8052866	3000160	SCOP2B (2022-06-29)
K [auth a]	SCOP2B Superfamily	Ufd2 core-like	8052864	3002149	SCOP2B (2022-06-29)
I [auth A]	SCOP2B Superfamily	Ufd2 core-like	8052864	3002149	SCOP2B (2022-06-29)
I [auth A]	SCOP2B Superfamily	RING/U-box like	8052866	3000160	SCOP2B (2022-06-29)
D [auth d]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
A [auth D]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
J [auth B], L [auth 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
I [auth A], K [auth a]	PF10408	Ubiquitin elongating factor core (Ufd2P_core)	Ubiquitin elongating factor core	-	Family
I [auth A], K [auth a]	PF04564	U-box domain (U-box)	U-box domain	The U-box is a domain of ~70 amino acids that is present in proteins from yeast to human. It consists of the beta-beta-alpha-beta-alpha- fold typical of U-box and RING domains. The central alpha helix is flanked by two prominent surface-exposed loop ...	The U-box is a domain of ~70 amino acids that is present in proteins from yeast to human. It consists of the beta-beta-alpha-beta-alpha- fold typical of U-box and RING domains. The central alpha helix is flanked by two prominent surface-exposed loop regions. This domain is one class of E3 ligases, involved in the ubiquitination process [1-3]. This domain is related to the Ring finger Pfam:PF00097 but lacks the zinc binding residues [4].	Domain
B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], H [auth c]	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
A [auth D], D [auth d]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
J [auth B], L [auth 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 anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide 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 protein-containing complex binding proteasome binding protein-macromolecule adaptor activity molecular adaptor activity	catabolic process proteolysis involved in protein catabolic process primary metabolic process 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 protein polyubiquitination catabolic process proteolysis involved in protein catabolic process primary metabolic process 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 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 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 cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus 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 ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ribosome-associated ubiquitin-dependent protein catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
I [auth A], K [auth a]	E4 ubiquitin-protein ligase UFD2	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-ubiquitin ligase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity	catabolic process proteolysis involved in protein catabolic process primary metabolic process 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 protein polyubiquitination catabolic process proteolysis involved in protein catabolic process primary metabolic process 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 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 cellular response to stimulus response to stimulus response to alcohol response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to alcohol response to chemical cellular response to ethanol response to ethanol response to nitrogen compound proteasomal protein catabolic process ERAD pathway cellular response to stress response to stress response to endoplasmic reticulum stress protein K48-linked ubiquitination regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process regulation of protein modification by small protein conjugation or removal positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of biological process regulation of post-translational protein modification regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process regulation of metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm 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
B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], H [auth c]	Ubiquitin	RNA binding binding nucleic acid binding structural molecule activity structural constituent of ribosome protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding cation binding transition metal ion binding zinc ion binding RNA binding binding nucleic acid binding structural molecule activity structural constituent of ribosome protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process macromolecule metabolic process protein metabolic process protein ubiquitination macromolecule modification catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process macromolecule metabolic process protein metabolic 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 biosynthetic process cytoplasmic translation translation gene expression macromolecule biosynthetic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytoplasm cytosol cell periphery plasma membrane nucleoplasm organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane endocytic vesicle cytosolic ribosome ribosome preribosome protein-containing complex ribonucleoprotein complex small-subunit processome synapse cell junction endosome membrane endosome mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cytosolic small ribosomal subunit small ribosomal subunit ribosomal subunit
A [auth D], D [auth d]	Polyubiquitin-C	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding RNA binding nucleic acid binding	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process macromolecule metabolic process protein metabolic process protein ubiquitination macromolecule modification catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process macromolecule metabolic process protein metabolic 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	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol endosome membrane endosome endomembrane system mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
J [auth B], L [auth b]	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
J [auth B], L [auth b]	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
J [auth B], L [auth b]	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
I [auth A], K [auth a]	IPR003613	U-box domain	Domain
I [auth A], K [auth a]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
I [auth A], K [auth a]	IPR045132	Ubiquitin conjugation factor E4	Family
I [auth A], K [auth a]	IPR019474	Ubiquitin conjugation factor E4, core	Domain
B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], H [auth c]	IPR019954	Ubiquitin conserved site	Conserved Site
B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], H [auth c]	IPR038582	Small ribosomal subunit protein eS31 eukaryotic superfamily	Homologous Superfamily
B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], H [auth c]	IPR050158	Ubiquitin and ubiquitin-like	Family
B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], H [auth c]	IPR011332	Zinc-binding ribosomal protein	Homologous Superfamily
B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], H [auth c]	IPR000626	Ubiquitin-like domain	Domain
B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], H [auth c]	IPR002906	Small ribosomal subunit protein eS31	Domain
B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], H [auth c]	IPR019956	Ubiquitin domain	Domain
B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], H [auth c]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A [auth D], D [auth d]	IPR019954	Ubiquitin conserved site	Conserved Site
A [auth D], D [auth d]	IPR000626	Ubiquitin-like domain	Domain
A [auth D], D [auth d]	IPR019956	Ubiquitin domain	Domain
A [auth D], D [auth d]	IPR050158	Ubiquitin and ubiquitin-like	Family
A [auth D], D [auth d]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], B [auth E], C [auth F], E [auth e], F [auth f], G [auth C], H [auth c]	Pharos: P62979	acute myeloid leukemia large cell medulloblastoma Diamond-Blackfan anemia lung carcinoma hematopoietic and lymphoid system neoplasm ulcerative colitis
A [auth D], D [auth d]	Pharos: P0CG48	acute myeloid leukemia heart disease myocardial infarction pancreatic ductal adenocarcinoma astrocytic tumor lung cancer osteosarcoma renal cell carcinoma glioblastoma malignant pancreatic neoplasm ovarian cancer