5Y3T | pdb_00005y3t

Crystal structure of hetero-trimeric core of LUBAC: HOIP double-UBA complexed with HOIL-1L UBL and SHARPIN UBL

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	HOIP UBA tandem repeat region-like	8088203	4004794	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	UBA-like	8092514	3001235	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	UBA-like	8092512	3001235	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	UBA-like	8092513	3001235	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)
C	PolyA_pol	e5y3tC1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains	T: Nucleotidyltransferase	F: PolyA_pol	ECOD (v294.1)
B	TBP	e5y3tB1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Ribosomal protein S5 domain 2-like	T: Ribosomal protein S5 domain 2-like	F: TBP	ECOD (v294.1)
A	PolyA_pol	e5y3tA1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains	T: Nucleotidyltransferase	F: PolyA_pol	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF25393	LUBAC thetering domain (LTM)	LUBAC thetering domain	This entry describes the Linear Ubiquitin Chain Assembly Complex (LUBAC)-tethering domain (LTM), which is located in the N-terminal region of the HOIL-1L protein in Eukaryotes. This domain facilitates interaction with SHARPIN, a key component in the ...	This entry describes the Linear Ubiquitin Chain Assembly Complex (LUBAC)-tethering domain (LTM), which is located in the N-terminal region of the HOIL-1L protein in Eukaryotes. This domain facilitates interaction with SHARPIN, a key component in the formation of the multi-protein E3 ubiquitin ligase LUBAC complex [1,2].	Domain
B	PF16678	HOIP UBA domain pair (UBA_HOIP)	HOIP UBA domain pair	-	Family
A	PF25393	LUBAC thetering domain (LTM)	LUBAC thetering domain	This entry describes the Linear Ubiquitin Chain Assembly Complex (LUBAC)-tethering domain (LTM), which is located in the N-terminal region of the HOIL-1L protein in Eukaryotes. This domain facilitates interaction with SHARPIN, a key component in the ...	This entry describes the Linear Ubiquitin Chain Assembly Complex (LUBAC)-tethering domain (LTM), which is located in the N-terminal region of the HOIL-1L protein in Eukaryotes. This domain facilitates interaction with SHARPIN, a key component in the formation of the multi-protein E3 ubiquitin ligase LUBAC complex [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Sharpin	protein binding binding ubiquitin binding ubiquitin-like protein binding protein-macromolecule adaptor activity molecular adaptor activity protein-containing complex binding polyubiquitin modification-dependent protein binding modification-dependent protein binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity protein binding binding ubiquitin binding ubiquitin-like protein binding protein-macromolecule adaptor activity molecular adaptor activity protein-containing complex binding polyubiquitin modification-dependent protein binding modification-dependent protein binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase 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 identical protein binding	protein polyubiquitination 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 linear polyubiquitination protein modification by small protein conjugation or removal cellular response to stimulus protein polyubiquitination 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 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 positive regulation of signaling cellular component disassembly cellular component organization execution phase of apoptosis cellular component disassembly involved in execution phase of apoptosis apoptotic nuclear changes apoptotic process cellular component organization or biogenesis cell death programmed cell death cell surface receptor signaling pathway regulation of CD40 signaling pathway CD40 signaling pathway regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus negative regulation of biological process response to external stimulus regulation of inflammatory response response to stress negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response developmental process epidermis development anatomical structure development tissue development defense response to bacterium biological process involved in interspecies interaction between organisms response to other organism response to bacterium response to external biotic stimulus response to biotic stimulus catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process multicellular organismal process epithelium development keratinization epidermal cell differentiation cellular developmental process animal organ development epithelial cell differentiation skin development cell differentiation keratinocyte differentiation response to cytokine cytokine-mediated signaling pathway response to peptide cellular response to tumor necrosis factor response to chemical tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus response to tumor necrosis factor organelle organization mitochondrion organization regulation of tumor necrosis factor-mediated signaling pathway regulation of cytokine-mediated signaling pathway regulation of response to cytokine stimulus	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol LUBAC complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex somatodendritic compartment cell projection dendrite dendritic tree cellular anatomical structure intracellular anatomical structure cytoplasm cytosol LUBAC complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection synapse cell junction glutamatergic synapse postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization organelle asymmetric synapse
B	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 cellular 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 protein polyubiquitination 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 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 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 negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process negative regulation of canonical NF-kappaB signal transduction negative regulation of cell communication negative regulation of cellular process negative regulation of response to stimulus negative regulation of signal transduction defense response to bacterium biological process involved in interspecies interaction between organisms response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus regulation of defense response regulation of response to biotic stimulus catabolic process regulation of response to external stimulus macroautophagy positive regulation of xenophagy autophagy xenophagy regulation of autophagy 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 regulation of catabolic process positive regulation of catabolic process regulation of macroautophagy defense response to other organism positive regulation of defense response regulation of metabolic process CD40 signaling pathway necroptotic process negative regulation of programmed cell death negative regulation of necroptotic process programmed necrotic cell death regulation of programmed cell death cell death regulation of necroptotic process negative regulation of programmed necrotic cell death regulation of programmed necrotic cell death programmed cell death response to cytokine cytokine-mediated signaling pathway response to peptide cellular response to tumor necrosis factor response to chemical tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus response to tumor necrosis factor	cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex signaling receptor complex CD40 receptor complex intracellular anatomical structure cytoplasm cytosol LUBAC complex cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex signaling receptor complex CD40 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
A	RanBP-type and C3HC4-type zinc finger-containing protein 1	enzyme regulator activity ubiquitin ligase activator activity enzyme activator activity ubiquitin-protein transferase regulator activity molecular function activator activity molecular function regulator activity ubiquitin-protein transferase activator activity protein binding binding ubiquitin binding ubiquitin-like protein binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein enzyme regulator activity ubiquitin ligase activator activity enzyme activator activity ubiquitin-protein transferase regulator activity molecular function activator activity molecular function regulator activity ubiquitin-protein transferase activator activity protein binding binding ubiquitin binding ubiquitin-like 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 DNA binding double-stranded DNA binding nucleic acid binding kinase binding protein kinase C binding enzyme binding protein kinase 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 cellular 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 protein polyubiquitination 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 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 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 positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death extrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway positive regulation of extrinsic apoptotic signaling pathway regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway regulation of apoptotic signaling pathway defense response to bacterium biological process involved in interspecies interaction between organisms response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process necroptotic process negative regulation of programmed cell death negative regulation of necroptotic process negative regulation of biological process programmed necrotic cell death regulation of necroptotic process negative regulation of programmed necrotic cell death negative regulation of cellular process regulation of programmed necrotic cell death regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction positive regulation of non-canonical NF-kappaB signal transduction response to cytokine cytokine-mediated signaling pathway response to peptide cellular response to tumor necrosis factor response to chemical tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus response to tumor necrosis factor positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process	LUBAC complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR011993	PH-like domain superfamily	Homologous Superfamily
C	IPR051628	Linear Ubiquitination-Associated E3 Ligases	Family
C	IPR031912	Sharpin, PH domain	Domain
C	IPR057468	HOIL-1/Sharpin, LUBAC thetering domain	Domain
C	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
C	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
C	IPR001876	Zinc finger, RanBP2-type	Domain
B	IPR002867	IBR domain	Domain
B	IPR044066	TRIAD supradomain	Domain
B	IPR036339	PUB-like domain superfamily	Homologous Superfamily
B	IPR026254	E3 ubiquitin-protein ligase RNF31-like	Family
B	IPR047541	E3 ubiquitin-protein ligase RNF31-like, modified RING finger, HC subclass	Domain
B	IPR057426	E3 ubiquitin-protein ligase RNF31, third UBA domain	Domain
B	IPR032065	E3 ubiquitin-protein ligase RNF31, UBA-like domain	Domain
B	IPR047539	E3 ubiquitin-protein ligase RNF31, UBA domain	Domain
B	IPR015940	Ubiquitin-associated domain	Domain
B	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
B	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
B	IPR018997	PUB domain	Domain
B	IPR047542	E3 ubiquitin-protein ligase RNF31-like, Rcat domain	Domain
B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B	IPR047543	E3 ubiquitin-protein ligase RNF31-like, Bbox1 zinc finger	Domain
B	IPR040641	E3 ubiquitin-protein ligase RNF31, PUB domain	Domain
B	IPR047540	E3 ubiquitin-protein ligase RNF31-like, BRcat domain	Domain
B	IPR001876	Zinc finger, RanBP2-type	Domain
B	IPR041031	RNF31, C-terminal	Domain
A	IPR044066	TRIAD supradomain	Domain
A	IPR047557	Heme-oxidized IRP2 ubiquitin ligase 1, Rcat domain	Domain
A	IPR051628	Linear Ubiquitination-Associated E3 Ligases	Family
A	IPR057468	HOIL-1/Sharpin, LUBAC thetering domain	Domain
A	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
A	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A	IPR000626	Ubiquitin-like domain	Domain
A	IPR027370	Zinc finger, RING-type, eukaryotic	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR047558	Heme-oxidized IRP2 ubiquitin ligase 1, BRcat domain	Domain
A	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A	IPR001876	Zinc finger, RanBP2-type	Domain
A	IPR001841	Zinc finger, RING-type	Domain
A	IPR047559	Heme-oxidized IRP2 ubiquitin ligase 1, modified RING finger, HC subclass	Domain