4WLP

Crystal structure of UCH37-NFRKB Inhibited Deubiquitylating Complex

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	NFRKB N-terminal domain-like	8091997	4007761	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Deubiquitinase adaptor domain (DEUBAD)-like	8091998	3002549	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	PF18031	e4wlpA2	A: alpha duplicates or obligate multimers	X: L27 domain (From Topology)	H: L27 domain (From Topology)	T: L27 domain	F: PF18031	ECOD (1.6)
A	PF01088	e4wlpA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF01088	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF18031	Ubiquitin carboxyl-terminal hydrolases (UCH_C)	Ubiquitin carboxyl-terminal hydrolases	This is the C-terminal domain found in eukaryotic UCH37 proteins (also known as Ubiquitin carboxyl-terminal hydrolase isozyme L5, UCHL5). UCH37 is a subunit of two complexes: INO80, which performs ATP-dependent sliding of nucleosomes for transcriptio ...	This is the C-terminal domain found in eukaryotic UCH37 proteins (also known as Ubiquitin carboxyl-terminal hydrolase isozyme L5, UCHL5). UCH37 is a subunit of two complexes: INO80, which performs ATP-dependent sliding of nucleosomes for transcriptional regulation and DNA repair, and the 26S proteasome, which performs ATP-dependent proteolysis of polyubiquitylated proteins in the cytosol and nucleus. Recruitment to the proteasome is mediated by the C-terminal domain of RPN13 (also known as ADRM1). Recruitment to INO80 is mediated by the N-terminal domain of NFRKB. Structural and biochemical analysis reveal that RPN13 and NFRKB make similar interactions with the UCH37 C-terminal domain but have very different interactions with the catalytic UCH domain that are activating in the case of RPN13 and highly inhibitory in the case of NFRKB [3].	Domain
A	PF01088	Ubiquitin carboxyl-terminal hydrolase, family 1 (Peptidase_C12)	Ubiquitin carboxyl-terminal hydrolase, family 1	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ubiquitin carboxyl-terminal hydrolase isozyme L5	RNA binding binding organic cyclic compound binding nucleic acid binding enzyme regulator activity molecular function inhibitor activity peptidase regulator activity molecular function regulator activity enzyme inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity cysteine-type peptidase activity ubiquitin-like protein peptidase activity RNA binding binding organic cyclic compound binding nucleic acid binding enzyme regulator activity molecular function inhibitor activity peptidase regulator activity molecular function regulator activity enzyme inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity protein-containing complex binding proteasome binding	developmental process multicellular organismal process head development animal organ development brain development nervous system development multicellular organism development central nervous system development midbrain development anatomical structure development system development regulation of biological process regulation of cellular component organization regulation of cellular process developmental process multicellular organismal process head development animal organ development brain development nervous system development multicellular organism development central nervous system development midbrain development anatomical structure development system development regulation of biological process regulation of cellular component organization regulation of cellular process biological regulation chromosome organization regulation of chromosome organization regulation of organelle organization cellular component organization organelle organization cellular process cellular component organization or biogenesis primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of metabolic process regulation of DNA replication regulation of DNA metabolic process lateral ventricle development forebrain development ventricular system development telencephalon development cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction cell communication positive regulation of response to stimulus positive regulation of smoothened signaling pathway signal transduction positive regulation of cellular process regulation of smoothened signaling pathway regulation of signaling cell surface receptor signaling pathway smoothened signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling regulation of cellular response to stress positive regulation of metabolic process positive regulation of DNA repair cellular response to stress response to stress regulation of response to stress positive regulation of macromolecule metabolic process DNA repair positive regulation of nucleobase-containing compound metabolic process regulation of DNA repair positive regulation of DNA metabolic process DNA damage response DNA recombination telomere organization telomere maintenance catabolic process negative regulation of proteolysis negative regulation of proteolysis involved in protein catabolic process proteolysis involved in protein catabolic process negative regulation of biological process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process negative regulation of protein catabolic process regulation of proteolysis involved in protein catabolic process regulation of proteolysis modification-dependent macromolecule catabolic process proteolysis protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of ubiquitin-dependent protein catabolic process organonitrogen compound catabolic process negative regulation of catabolic process negative regulation of proteasomal ubiquitin-dependent protein catabolic process organonitrogen compound metabolic process regulation of protein metabolic process negative regulation of metabolic process proteasomal protein catabolic process protein catabolic process regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process negative regulation of proteasomal protein catabolic process regulation of proteasomal protein catabolic process ubiquitin-dependent protein catabolic process organic substance catabolic process regulation of protein catabolic process brain morphogenesis forebrain morphogenesis anatomical structure morphogenesis animal organ morphogenesis positive regulation of macromolecule biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process cellular metabolic process regulation of cellular metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription cellular biosynthetic process RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process protein deubiquitination protein modification by small protein removal macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation or removal regulation of embryonic development regulation of multicellular organismal development regulation of developmental process embryo development regulation of multicellular organismal process cell cycle regulation of cell cycle positive regulation of organelle organization telomere maintenance in response to DNA damage positive regulation of telomere maintenance positive regulation of chromosome organization regulation of telomere maintenance positive regulation of cellular component organization positive regulation of telomere maintenance in response to DNA damage regulation of telomere maintenance in response to DNA damage regulation of DNA strand elongation DNA strand elongation protein-DNA complex organization protein-containing complex organization chromatin organization chromatin remodeling	membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle SWI/SNF superfamily-type complex non-membrane-bounded organelle INO80-type complex membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle SWI/SNF superfamily-type complex non-membrane-bounded organelle INO80-type complex catalytic complex protein-DNA complex chromatin intracellular membrane-bounded organelle cellular anatomical entity Ino80 complex organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen nucleolus cytoplasm cytosol nucleoplasm peptidase complex cytosolic proteasome complex proteasome complex endopeptidase complex intracellular protein-containing complex
B	Nuclear factor related to kappa-B-binding protein	DNA binding binding organic cyclic compound binding nucleic acid binding protein binding enzyme binding protease binding	regulation of biological process regulation of cellular component organization regulation of cellular process biological regulation chromosome organization regulation of chromosome organization regulation of organelle organization cellular component organization organelle organization cellular process cellular component organization or biogenesis cellular response to stimulus response to stimulus primary metabolic process regulation of biological process regulation of cellular component organization regulation of cellular process biological regulation chromosome organization regulation of chromosome organization regulation of organelle organization cellular component organization organelle organization cellular process cellular component organization or biogenesis cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process macromolecule metabolic process DNA repair positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process regulation of cellular metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process positive regulation of cellular 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 regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process DNA replication regulation of DNA replication regulation of DNA metabolic process developmental process multicellular organismal process regulation of embryonic development regulation of multicellular organismal development regulation of developmental process embryo development multicellular organism development anatomical structure development regulation of multicellular organismal process cell cycle regulation of cell cycle positive regulation of organelle organization telomere maintenance in response to DNA damage regulation of cellular response to stress telomere organization positive regulation of telomere maintenance positive regulation of chromosome organization telomere maintenance positive regulation of DNA metabolic process regulation of response to stimulus regulation of telomere maintenance positive regulation of cellular component organization positive regulation of response to stimulus regulation of response to stress positive regulation of telomere maintenance in response to DNA damage regulation of telomere maintenance in response to DNA damage regulation of DNA repair regulation of DNA strand elongation DNA strand elongation positive regulation of DNA repair DNA recombination protein-DNA complex organization protein-containing complex organization chromatin organization chromatin remodeling	membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle SWI/SNF superfamily-type complex non-membrane-bounded organelle INO80-type complex membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle SWI/SNF superfamily-type complex non-membrane-bounded organelle INO80-type complex catalytic complex protein-DNA complex chromatin intracellular membrane-bounded organelle cellular anatomical entity Ino80 complex organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR033837	Ubiquitinyl hydrolase-L5	Domain
A	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A	IPR017390	Ubiquitinyl hydrolase, UCH37 type	Family
A	IPR001578	Peptidase C12, ubiquitin carboxyl-terminal hydrolase	Domain
A	IPR041507	Peptidase C12, C-terminal domain	Domain
A	IPR036959	Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily	Homologous Superfamily
B	IPR025220	NFRKB winged helix-like domain	Domain
B	IPR044867	DEUBAD domain	Domain
B	IPR038106	NFRKB winged helix-like domain superfamily	Homologous Superfamily
B	IPR024867	Nuclear factor related to kappa-B-binding protein	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9Y5K5	astrocytic tumor lung cancer ovarian cancer hereditary spastic paraplegia non-small cell lung carcinoma psoriasis invasive ductal breast carcinoma oligodendroglioma
B	Pharos: Q6P4R8	lung cancer osteosarcoma malignant ependymoma psoriasis malignant mesothelioma

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.