4QPL | pdb_00004qpl

Crystal structure of RNF146(RING-WWE)/UbcH5a/iso-ADPr complex

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)
D	d4qpld1	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4qpld2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4qplb1	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4qplb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
D	SCOP2B Superfamily	UBC-like	8059970	3000570	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	UBC-like	8059970	3000570	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	WWE domain	8042859	3001237	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	WWE domain	8042859	3001237	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)
D	Methyltrn_RNA_3	e4qplD1	A: a/b three-layered sandwiches	X: Insertion subdomain in DsbA-like	H: Insertion subdomain in DsbA-like	T: Insertion subdomain in DsbA-like	F: Methyltrn_RNA_3	ECOD (v294.1)
B	Methyltrn_RNA_3	e4qplB1	A: a/b three-layered sandwiches	X: Insertion subdomain in DsbA-like	H: Insertion subdomain in DsbA-like	T: Insertion subdomain in DsbA-like	F: Methyltrn_RNA_3	ECOD (v294.1)
C	TibC_1st	e4qplC1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: TibC_1st	ECOD (v294.1)
A	Methyltrn_RNA_3	e4qplA1	A: a/b three-layered sandwiches	X: Insertion subdomain in DsbA-like	H: Insertion subdomain in DsbA-like	T: Insertion subdomain in DsbA-like	F: Methyltrn_RNA_3	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
B	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
C	3.30.720.50	Alpha Beta	2-Layer Sandwich	Signal recognition particle alu RNA binding heterodimer, srp9/1		CATH (utative)
A	3.30.720.50	Alpha Beta	2-Layer Sandwich	Signal recognition particle alu RNA binding heterodimer, srp9/1		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	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
A, C	PF02825	WWE domain (WWE)	WWE domain	The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems [1].	Domain
A, C	PF13920	Zinc finger, C3HC4 type (RING finger) (zf-C3HC4_3)	Zinc finger, C3HC4 type (RING finger)		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	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 primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process protein polyubiquitination protein ubiquitination macromolecule modification catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule 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
A, C	E3 ubiquitin-protein ligase RNF146	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 poly-ADP-D-ribose binding binding carbohydrate derivative binding cation binding transition metal ion 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 poly-ADP-D-ribose binding binding carbohydrate derivative binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding protein binding enzyme binding	protein autoubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process 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 regulation of cellular process protein autoubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process 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 regulation of cellular process response to stimulus cellular response to oxidative stress regulation of cellular response to stress negative regulation of biological process cellular response to chemical stress regulation of cellular response to oxidative stress cellular response to stress response to stress regulation of response to stress regulation of response to oxidative stress negative regulation of cellular process negative regulation of response to oxidative stress negative regulation of cellular response to oxidative stress regulation of biological process negative regulation of response to stimulus biological regulation response to oxidative stress cellular response to chemical stimulus regulation of response to stimulus response to chemical catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide cellular response to reactive oxygen species protein polyubiquitination protein K48-linked ubiquitination cell surface receptor signaling pathway signaling cell communication signal transduction Wnt signaling pathway positive regulation of cell communication positive regulation of signal transduction regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway positive regulation of biological process regulation of signal transduction positive regulation of response to stimulus positive regulation of Wnt signaling pathway positive regulation of cellular process positive regulation of canonical Wnt signaling pathway regulation of signaling regulation of Wnt signaling pathway regulation of cell communication positive regulation of signaling	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
B, D	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
B, D	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
A, C	IPR033509	E3 ubiquitin-protein ligase RNF146	Family
A, C	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A, C	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, C	IPR004170	WWE domain	Domain
A, C	IPR044110	RNF146, RING finger, HC subclass	Domain
A, C	IPR037197	WWE domain superfamily	Homologous Superfamily
A, C	IPR018123	WWE domain, subgroup	Domain
A, C	IPR001841	Zinc finger, RING-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.