3B08 | pdb_00003b08

Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin

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)
A	d3b08a1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth D]	d3b08d1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth G]	d3b08g1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G [auth J]	d3b08j1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	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)
A	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
E [auth G]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
G [auth J]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ran binding protein zinc finger-like	8088591	3000133	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Ran binding protein zinc finger-like	8088591	3000133	SCOP2B (2022-06-29)
F [auth H]	SCOP2B Superfamily	Ran binding protein zinc finger-like	8088591	3000133	SCOP2B (2022-06-29)
H [auth K]	SCOP2B Superfamily	Ran binding protein zinc finger-like	8088591	3000133	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	ubiquitin_1	e3b08A1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
C [auth D]	ubiquitin_1	e3b08D1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
E [auth G]	ubiquitin_1	e3b08G1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
G [auth J]	ubiquitin_1	e3b08J1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
B	zf-RanBP	e3b08B1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: zf-RanBP	ECOD (1.6)
D [auth E]	zf-RanBP	e3b08E1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: zf-RanBP	ECOD (1.6)
F [auth H]	zf-RanBP	e3b08H1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: zf-RanBP	ECOD (1.6)
H [auth K]	zf-RanBP	e3b08K1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: zf-RanBP	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C [auth D]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
E [auth G]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
G [auth J]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	2.30.30.380	Mainly Beta	Roll	SH3 type barrels.	Zn-finger domain of Sec23/24	CATH (4.3.0)
D [auth E]	2.30.30.380	Mainly Beta	Roll	SH3 type barrels.	Zn-finger domain of Sec23/24	CATH (4.3.0)
F [auth H]	2.30.30.380	Mainly Beta	Roll	SH3 type barrels.	Zn-finger domain of Sec23/24	CATH (4.3.0)
H [auth K]	2.30.30.380	Mainly Beta	Roll	SH3 type barrels.	Zn-finger domain of Sec23/24	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth D], E [auth G], G [auth J]	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, C [auth D], E [auth G], G [auth J]	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
B, D [auth E], F [auth H], H [auth K]	RanBP-type and C3HC4-type zinc finger-containing protein 1	aminoacyltransferase activity enzyme regulator activity ubiquitin-protein transferase regulator activity catalytic activity, acting on a protein acyltransferase activity molecular function activator activity transferase activity ubiquitin-protein transferase activator activity ubiquitin-protein transferase activity ubiquitin-like protein transferase activity ubiquitin ligase activator activity enzyme activator activity molecular function regulator activity catalytic activity aminoacyltransferase activity enzyme regulator activity ubiquitin-protein transferase regulator activity catalytic activity, acting on a protein acyltransferase activity molecular function activator activity transferase activity ubiquitin-protein transferase activator activity ubiquitin-protein transferase activity ubiquitin-like protein transferase activity ubiquitin ligase activator activity enzyme activator activity molecular function regulator activity catalytic activity protein binding binding ubiquitin binding ubiquitin-like protein binding cation 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 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 catabolic process proteolysis involved in protein 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 proteolysis 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	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
A, C [auth D], E [auth G], G [auth J]	IPR019954	Ubiquitin conserved site	Conserved Site
A, C [auth D], E [auth G], G [auth J]	IPR000626	Ubiquitin-like domain	Domain
A, C [auth D], E [auth G], G [auth J]	IPR019956	Ubiquitin domain	Domain
A, C [auth D], E [auth G], G [auth J]	IPR050158	Ubiquitin and ubiquitin-like	Family
A, C [auth D], E [auth G], G [auth J]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B, D [auth E], F [auth H], H [auth K]	IPR044066	TRIAD supradomain	Domain
B, D [auth E], F [auth H], H [auth K]	IPR047557	Heme-oxidized IRP2 ubiquitin ligase 1, Rcat domain	Domain
B, D [auth E], F [auth H], H [auth K]	IPR051628	Linear Ubiquitination-Associated E3 Ligases	Family
B, D [auth E], F [auth H], H [auth K]	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
B, D [auth E], F [auth H], H [auth K]	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
B, D [auth E], F [auth H], H [auth K]	IPR000626	Ubiquitin-like domain	Domain
B, D [auth E], F [auth H], H [auth K]	IPR027370	Zinc finger, RING-type, eukaryotic	Domain
B, D [auth E], F [auth H], H [auth K]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B, D [auth E], F [auth H], H [auth K]	IPR047558	Heme-oxidized IRP2 ubiquitin ligase 1, BRcat domain	Domain
B, D [auth E], F [auth H], H [auth K]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B, D [auth E], F [auth H], H [auth K]	IPR001876	Zinc finger, RanBP2-type	Domain
B, D [auth E], F [auth H], H [auth K]	IPR001841	Zinc finger, RING-type	Domain
B, D [auth E], F [auth H], H [auth K]	IPR047559	Heme-oxidized IRP2 ubiquitin ligase 1, modified RING finger, HC subclass	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C [auth D], E [auth G], G [auth J]	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

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.