5WQ4

Crystal structure of OPTN and linear diubiquitin complex

External Resource: Annotation

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

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth B]	d5wq4b1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth A]	d5wq4a1	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 [auth B]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
B [auth C]	SCOP2 Family	NEMO CC2-LZ-like	8067903	4004622	SCOP2 (2022-06-29)
B [auth C]	SCOP2 Superfamily	NEMO CC2-LZ-like	8090866	3002465	SCOP2 (2022-06-29)
C [auth D]	SCOP2B Superfamily	NEMO CC2-LZ-like	8090866	3002465	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	NEMO CC2-LZ-like	8090866	3002465	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	NEMO CC2-LZ-like	8090866	3002465	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 [auth B]	ubiquitin_1	e5wq4B2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
D [auth A]	ubiquitin_1	e5wq4A2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
D [auth A]	ubiquitin	e5wq4A1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], D [auth A]	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
B [auth C], C [auth D], E, F	PF16516	Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator (CC2-LZ)	Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator	-	Coiled-coil

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], D [auth A]	ubiquitin	protein binding binding enzyme binding protease binding protein tag activity molecular tag activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding RNA binding organic cyclic compound binding nucleic acid binding	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic 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 cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle 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 cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle 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 [auth C], C [auth D], E, F	Optineurin	transcription factor binding protein binding binding RNA polymerase III general transcription initiation factor binding general transcription initiation factor binding TFIIIA-class transcription factor binding ubiquitin binding ubiquitin-like protein binding polyubiquitin modification-dependent protein binding modification-dependent protein binding K63-linked polyubiquitin modification-dependent protein binding protein-macromolecule adaptor activity molecular adaptor activity cation binding transcription factor binding protein binding binding RNA polymerase III general transcription initiation factor binding general transcription initiation factor binding TFIIIA-class transcription factor binding ubiquitin binding ubiquitin-like protein binding polyubiquitin modification-dependent protein binding modification-dependent protein binding K63-linked polyubiquitin modification-dependent protein binding protein-macromolecule adaptor activity molecular adaptor activity cation binding ion binding metal ion binding small molecule binding identical protein binding	protein localization Golgi to plasma membrane transport establishment of protein localization cellular localization nitrogen compound transport post-Golgi vesicle-mediated transport transport establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport vesicle-mediated transport localization cellular macromolecule localization protein localization to cell periphery establishment of protein localization to membrane protein localization Golgi to plasma membrane transport establishment of protein localization cellular localization nitrogen compound transport post-Golgi vesicle-mediated transport transport establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport vesicle-mediated transport localization cellular macromolecule localization protein localization to cell periphery establishment of protein localization to membrane protein localization to plasma membrane organic substance transport localization within membrane protein localization to membrane establishment of localization vesicle-mediated transport to the plasma membrane protein transport macromolecule localization cellular process Golgi vesicle transport regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation biological regulation positive regulation of biological process positive regulation of neural precursor cell proliferation regulation of cell population proliferation neural precursor cell proliferation positive regulation of cellular process regulation of neural precursor cell proliferation cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process cellular response to stimulus response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process negative regulation of canonical NF-kappaB signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process signal transduction regulation of signaling negative regulation of response to stimulus negative regulation of signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction cellular catabolic process catabolic process autophagy process utilizing autophagic mechanism biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus neuron apoptotic process positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process positive regulation of neuron apoptotic process programmed cell death regulation of neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death negative regulation of apoptotic process regulation of defense response regulation of response to biotic stimulus regulation of response to external stimulus macroautophagy positive regulation of xenophagy xenophagy regulation of autophagy positive regulation of response to stimulus positive regulation of response to external stimulus regulation of response to stress positive regulation of macroautophagy positive regulation of autophagy regulation of xenophagy 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 negative regulation of cell population proliferation protein localization to Golgi apparatus protein localization to organelle regulation of receptor recycling negative regulation of receptor recycling negative regulation of metabolic process receptor recycling receptor metabolic process negative regulation of macromolecule metabolic process defense response to Gram-negative bacterium defense response to bacterium response to bacterium multicellular organismal process cytokine production regulation of cytokine production regulation of multicellular organismal process positive regulation of multicellular organismal process positive regulation of cytokine production cellular component organization organelle organization Golgi ribbon formation cellular component organization or biogenesis Golgi organization endomembrane system organization response to organic substance cellular response to topologically incorrect protein cellular response to unfolded protein response to unfolded protein cellular response to chemical stimulus cellular response to stress response to chemical response to topologically incorrect protein cellular response to organic substance mitophagy organelle disassembly mitochondrion organization cellular component disassembly regulation of autophagy of mitochondrion in response to mitochondrial depolarization positive regulation of mitophagy in response to mitochondrial depolarization response to mitochondrial depolarisation positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization autophagy of mitochondrion parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle intracellular vesicle intracellular membrane-bounded organelle vesicle vacuole autophagosome Golgi apparatus subcompartment intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle intracellular vesicle intracellular membrane-bounded organelle vesicle vacuole autophagosome Golgi apparatus subcompartment Golgi apparatus organelle subcompartment endomembrane system trans-Golgi network endosome recycling endosome perinuclear region of cytoplasm somatodendritic compartment cell body neuronal cell body axon cell projection neuron projection plasma membrane bounded cell projection nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], D [auth A]	IPR019954	Ubiquitin conserved site	Conserved Site
A [auth B], D [auth A]	IPR000626	Ubiquitin-like domain	Domain
A [auth B], D [auth A]	IPR019956	Ubiquitin domain	Domain
A [auth B], D [auth A]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B [auth C], C [auth D], E, F	IPR034735	NEMO, Zinc finger	Domain
B [auth C], C [auth D], E, F	IPR021063	NF-kappa-B essential modulator NEMO, N-terminal	Domain
B [auth C], C [auth D], E, F	IPR032419	NF-kappa-B essential modulator NEMO, CC2-LZ domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B], D [auth A]	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 National Science Foundation (DBI-1832184), 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 R01GM133198.