4LJO

Structure of an active ligase (HOIP)/ubiquitin transfer 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)
B	d4ljob_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Ubiquitin-related	8098885	4000962	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Ubiquitin-like	8098886	3000157	SCOP2 (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	IBR_1	e4ljoA1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: IBR domain	F: IBR_1	ECOD (1.6)
A	EUF08754	e4ljoA2	A: few secondary structure elements	X: E3 ligase HOIP C-terminal domain (From Topology)	H: E3 ligase HOIP C-terminal domain (From Topology)	T: E3 ligase HOIP C-terminal domain	F: EUF08754	ECOD (1.6)
B	ubiquitin_1	e4ljoB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF18091	E3 Ubiquitin Ligase RBR C-terminal domain (E3_UbLigase_RBR)	E3 Ubiquitin Ligase RBR C-terminal domain	This is the C-terminal domain of HOIP present in Homo sapiens. HOIP synthesize the linear ubiquitin chains that help control innate immunity and inflammation. This region has an RBR domain which catalyzes the transfer of ubiquitin onto a substrate [1 ...	This is the C-terminal domain of HOIP present in Homo sapiens. HOIP synthesize the linear ubiquitin chains that help control innate immunity and inflammation. This region has an RBR domain which catalyzes the transfer of ubiquitin onto a substrate [1].	Domain
A	PF22191	IBR domain (IBR_1)	IBR domain	This entry represents an IBR domain, related to Pfam:PF01485.	Domain
B	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
A	E3 ubiquitin-protein ligase RNF31	polyubiquitin modification-dependent protein binding protein binding binding K48-linked polyubiquitin modification-dependent protein binding modification-dependent protein binding ubiquitin binding ubiquitin-like protein binding linear polyubiquitin binding K63-linked polyubiquitin modification-dependent protein binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity polyubiquitin modification-dependent protein binding protein binding binding K48-linked polyubiquitin modification-dependent protein binding modification-dependent protein binding ubiquitin binding ubiquitin-like protein binding linear polyubiquitin binding K63-linked polyubiquitin modification-dependent protein 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 ubiquitin protein ligase 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 identical protein binding	protein polyubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein linear polyubiquitination protein modification by small protein conjugation or removal cellular response to stimulus positive regulation of cell communication protein polyubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein linear polyubiquitination protein modification by small protein conjugation or removal cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction cellular process positive regulation of signaling immune response-regulating cell surface receptor signaling pathway immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response T cell receptor signaling pathway immune system process regulation of immune response antigen receptor-mediated signaling pathway activation of immune response biological process involved in interspecies interaction between organisms response to other organism defense response response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus protein localization regulation of localization establishment of protein localization cellular localization regulation of protein localization protein targeting regulation of protein targeting to mitochondrion positive regulation of establishment of protein localization localization cellular macromolecule localization positive regulation of protein targeting to mitochondrion regulation of establishment of protein localization establishment of localization regulation of establishment of protein localization to mitochondrion establishment of protein localization to organelle regulation of protein targeting regulation of cellular localization macromolecule localization protein localization to organelle protein localization to mitochondrion positive regulation of protein localization protein targeting to mitochondrion establishment of protein localization to mitochondrion positive regulation of establishment of protein localization to mitochondrion regulation of defense response regulation of response to biotic stimulus catabolic process regulation of response to external stimulus macroautophagy positive regulation of xenophagy autophagy positive regulation of cellular metabolic process xenophagy regulation of autophagy cellular catabolic process positive regulation of metabolic process positive regulation of response to external stimulus regulation of response to stress positive regulation of macroautophagy process utilizing autophagic mechanism positive regulation of autophagy regulation of xenophagy cellular metabolic process regulation of cellular metabolic process regulation of catabolic process positive regulation of catabolic process regulation of macroautophagy regulation of cellular catabolic process positive regulation of defense response positive regulation of cellular catabolic process regulation of metabolic process CD40 signaling pathway necroptotic process negative regulation of programmed cell death negative regulation of necroptotic process negative regulation of biological process programmed necrotic cell death regulation of programmed cell death cell death regulation of necroptotic process negative regulation of programmed necrotic cell death negative regulation of cellular process regulation of programmed necrotic cell death programmed cell death positive regulation of DNA-binding transcription factor activity cellular biosynthetic process positive regulation of NF-kappaB transcription factor activity RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process positive regulation of molecular function nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process regulation of molecular function regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity regulation of macromolecule biosynthetic process regulation of DNA-templated transcription	cell periphery protein-containing complex plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex CD40 receptor complex cellular anatomical entity receptor complex intracellular anatomical structure cytoplasm cytosol LUBAC complex cell periphery protein-containing complex plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex CD40 receptor complex cellular anatomical entity receptor complex intracellular anatomical structure cytoplasm cytosol LUBAC complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane
B	Polyubiquitin-C	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding structural molecule activity structural constituent of ribosome	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 protein metabolic process macromolecule metabolic process protein ubiquitination macromolecule modification post-translational protein 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 protein metabolic process macromolecule 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 cellular biosynthetic process cellular metabolic process translation gene expression macromolecule biosynthetic process biosynthetic process cellular process	synapse cell junction cellular anatomical entity protein-containing complex intracellular anatomical structure intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome cytoplasm synapse cell junction cellular anatomical entity protein-containing complex intracellular anatomical structure intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome cytoplasm cytosol large ribosomal subunit non-membrane-bounded organelle cell periphery plasma membrane membrane cytosolic small ribosomal subunit small ribosomal subunit membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen endoplasmic reticulum endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002867	IBR domain	Domain
A	IPR044066	TRIAD supradomain	Domain
A	IPR036339	PUB-like domain superfamily	Homologous Superfamily
A	IPR026254	E3 ubiquitin-protein ligase RNF31-like	Family
A	IPR047541	E3 ubiquitin-protein ligase RNF31-like, modified RING finger, HC subclass	Domain
A	IPR032065	E3 ubiquitin-protein ligase RNF31, UBA-like domain	Domain
A	IPR047539	E3 ubiquitin-protein ligase RNF31, UBA domain	Domain
A	IPR015940	Ubiquitin-associated domain	Domain
A	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
A	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A	IPR018997	PUB domain	Domain
A	IPR047542	E3 ubiquitin-protein ligase RNF31-like, Rcat domain	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR047543	E3 ubiquitin-protein ligase RNF31-like, Bbox1 zinc finger	Domain
A	IPR040641	E3 ubiquitin-protein ligase RNF31, PUB domain	Domain
A	IPR047540	E3 ubiquitin-protein ligase RNF31-like, BRcat domain	Domain
A	IPR001876	Zinc finger, RanBP2-type	Domain
A	IPR041031	RNF31, C-terminal	Domain
B	IPR019954	Ubiquitin conserved site	Conserved Site
B	IPR038587	Large ribosomal subunit protein eL40 superfamily	Homologous Superfamily
B	IPR000626	Ubiquitin-like domain	Domain
B	IPR019956	Ubiquitin domain	Domain
B	IPR050158	Ubiquitin and ubiquitin-like	Family
B	IPR001975	Large ribosomal subunit protein eL40 domain	Domain
B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily