2YHO | pdb_00002yho

The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2yhob1	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2yhob2	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2yhod1	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2yhod2	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d2yhof1	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d2yhof2	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d2yhoh_	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	UBC-like	8059970	3000570	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	UBC-like	8059970	3000570	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	UBC-like	8059970	3000570	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	UBC-like	8059970	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	zf-C3HC4_3	e2yhoA1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-C3HC4_3	ECOD (1.6)
C	zf-C3HC4_3	e2yhoC1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-C3HC4_3	ECOD (1.6)
E	zf-C3HC4_3	e2yhoE1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-C3HC4_3	ECOD (1.6)
G	zf-C3HC4_3	e2yhoG1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-C3HC4_3	ECOD (1.6)
B	UQ_con	e2yhoB1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: UQ_con	ECOD (1.6)
D	UQ_con	e2yhoD1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: UQ_con	ECOD (1.6)
F	UQ_con	e2yhoF1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: UQ_con	ECOD (1.6)
H	UQ_con	e2yhoH1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: UQ_con	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
C	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
E	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
G	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
B	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
D	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
F	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
H	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, C, E, G	PF13920	Zinc finger, C3HC4 type (RING finger) (zf-C3HC4_3)	Zinc finger, C3HC4 type (RING finger)		Domain
B, D, F, H	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, C, E, G	E3 UBIQUITIN-PROTEIN LIGASE MYLIP	cytoskeletal protein binding protein binding 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 transition metal ion binding cytoskeletal protein binding protein binding 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 transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	protein destabilization regulation of protein stability biological regulation regulation of biological quality regulation of cellular process catabolic process positive regulation of protein metabolic process positive regulation of biological process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process protein destabilization regulation of protein stability biological regulation regulation of biological quality regulation of cellular process catabolic process positive regulation of protein metabolic process positive regulation of biological process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biological process regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process sterol homeostasis chemical homeostasis homeostatic process cholesterol homeostasis lipid homeostasis 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 regulation of neuron projection development multicellular organismal process regulation of cellular component organization cellular developmental process cell projection organization negative regulation of biological process cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process cellular component organization or biogenesis negative regulation of cell projection organization system development developmental process plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization nervous system development negative regulation of neuron projection development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process regulation of plasma lipoprotein particle levels regulation of low-density lipoprotein particle clearance negative regulation of low-density lipoprotein particle clearance plasma lipoprotein particle clearance negative regulation of lipoprotein particle clearance regulation of lipoprotein particle clearance regulation of multicellular organismal process low-density lipoprotein particle clearance negative regulation of multicellular organismal process receptor catabolic process receptor metabolic process regulation of low-density lipoprotein particle receptor catabolic process low-density lipoprotein particle receptor catabolic process low-density lipoprotein receptor particle metabolic process regulation of receptor catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane intracellular organelle cytoskeleton organelle membraneless organelle intracellular membraneless organelle
B, D, F, H	UBIQUITIN-CONJUGATING ENZYME E2 D1	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 ubiquitin-like protein ligase activity ubiquitin protein ligase 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 protein K48-linked ubiquitination cellular response to stimulus regulation of cellular process response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication negative regulation of TORC1 signaling regulation of intracellular signal transduction negative regulation of TOR signaling negative regulation of cellular process signal transduction regulation of TORC1 signaling TOR signaling regulation of biological process regulation of signaling regulation of TOR signaling negative regulation of response to stimulus biological regulation negative regulation of signal transduction regulation of response to stimulus regulation of cell communication TORC1 signaling 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 post-translational protein modification regulation of protein metabolic process regulation of macromolecule metabolic process regulation of metabolic process RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of cellular response to growth factor stimulus negative regulation of BMP signaling pathway cellular response to endogenous stimulus BMP signaling pathway enzyme-linked receptor protein signaling pathway cellular response to BMP stimulus cell surface receptor signaling pathway regulation of BMP signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus response to BMP transforming growth factor beta receptor superfamily signaling pathway response to growth factor negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway regulation of protein polyubiquitination positive regulation of protein polyubiquitination proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR000299	FERM domain	Domain
A, C, E, G	IPR014352	FERM/acyl-CoA-binding protein superfamily	Homologous Superfamily
A, C, E, G	IPR019748	FERM central domain	Domain
A, C, E, G	IPR018980	FERM, C-terminal PH-like domain	Domain
A, C, E, G	IPR000798	Ezrin/radixin/moesin-like	Family
A, C, E, G	IPR011993	PH-like domain superfamily	Homologous Superfamily
A, C, E, G	IPR019749	Band 4.1 domain	Domain
A, C, E, G	IPR035963	FERM superfamily, second domain	Homologous Superfamily
A, C, E, G	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, C, E, G	IPR041790	MYLIP, FERM domain C-lobe	Domain
A, C, E, G	IPR018979	FERM, N-terminal	Domain
A, C, E, G	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, C, E, G	IPR001841	Zinc finger, RING-type	Domain
B, D, F, H	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
B, D, F, H	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
B, D, F, H	IPR000608	Ubiquitin-conjugating enzyme E2, catalytic core domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G	Pharos: Q8WY64	endometriosis acute myeloid leukemia Endometrioma malignant glioma medulloblastoma tuberculosis adrenal cortex carcinoma large cell medulloblastoma malignant mesothelioma osteosarcoma ulcerative colitis atypical teratoid rhabdoid tumor exocrine pancreatic carcinoma lung adenocarcinoma malignant pancreatic neoplasm endometriosis acute myeloid leukemia Endometrioma malignant glioma medulloblastoma tuberculosis adrenal cortex carcinoma large cell medulloblastoma malignant mesothelioma osteosarcoma ulcerative colitis atypical teratoid rhabdoid tumor exocrine pancreatic carcinoma lung adenocarcinoma malignant pancreatic neoplasm ovarian cancer
B, D, F, H	Pharos: P51668	adenoma Duchenne muscular dystrophy malignant mesothelioma ovarian cancer Crohn disease inflammatory bowel disease medulloblastoma sarcoidosis cutaneous lupus erythematosus limb-girdle muscular dystrophy myopathy

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.