9E7K | pdb_00009e7k

Crystal structure of the UCH37 RPN13 DEUBAD complex bound to an inhibitory nanobody in the canonical ubiquitin binding site

External Resource: Annotation

Domain Annotation: SCOP2 Classification
SAbDab Antibody Annotation
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)
C [auth B]	SCOP2B Superfamily	Deubiquitinase adaptor domain (DEUBAD)-like	8091996	3002549	SCOP2B (2022-06-29)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth C]	Heavy Chain	IGHV1	-	isoform 3 of ubiquitin carboxyl-terminal hydrolase isozymel5 \| proteasomal ubiquitin receptor adrm1	SAbDab (2025-12-05)

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
C [auth B]	Proteasomal ubiquitin receptor ADRM1	molecular function inhibitor activity molecular function regulator activity protein binding binding enzyme binding protease binding protein-containing complex binding proteasome binding endopeptidase activator activity enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity peptidase activator activity molecular function inhibitor activity molecular function regulator activity protein binding binding enzyme binding protease binding protein-containing complex binding proteasome binding endopeptidase activator activity enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity peptidase activator activity endopeptidase regulator activity	cellular component organization cellular component biogenesis proteasome assembly cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis transcription elongation by RNA polymerase II RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process cellular component organization cellular component biogenesis proteasome assembly cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis transcription elongation by RNA polymerase II RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process DNA-templated transcription elongation transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process 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 protein metabolic process	protein-containing complex catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane proteasome regulatory particle protein-containing complex catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane proteasome regulatory particle proteasome regulatory particle, lid subcomplex proteasome accessory complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
B [auth C]	Nb-cS1	-	-	-
A	Isoform 3 of Ubiquitin carboxyl-terminal hydrolase isozyme L5	RNA binding 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 RNA binding 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 DNA replication 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 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 negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of ubiquitin-dependent protein catabolic process negative regulation of catabolic process negative regulation of proteasomal ubiquitin-dependent protein catabolic 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 regulation of protein catabolic process brain morphogenesis forebrain morphogenesis anatomical structure morphogenesis animal organ morphogenesis positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic 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 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 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 regulation of telomere maintenance telomere maintenance in response to DNA damage positive regulation of cellular component organization positive regulation of telomere maintenance in response to DNA damage positive regulation of telomere maintenance regulation of telomere maintenance in response to DNA damage positive regulation of chromosome organization regulation of DNA strand elongation DNA strand elongation 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 cellular anatomical structure membraneless organelle SWI/SNF superfamily-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 cellular anatomical structure membraneless organelle SWI/SNF superfamily-type complex INO80-type complex catalytic complex intracellular membraneless organelle chromatin intracellular membrane-bounded organelle Ino80 complex organelle lumen organelle nuclear lumen nucleolus cytoplasm cytosol nucleoplasm peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth B]	IPR044868	Rpn13/ADRM1, Pru domain	Domain
C [auth B]	IPR038108	RPN13, DEUBAD domain superfamily	Homologous Superfamily
C [auth B]	IPR032368	RPN13, DEUBAD domain	Domain
C [auth B]	IPR006773	Proteasomal ubiquitin receptor Rpn13/ADRM1	Family
C [auth B]	IPR038633	Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily	Homologous Superfamily
C [auth B]	IPR044867	DEUBAD domain	Domain
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth B]	Pharos: Q16186	colorectal adenoma ovarian cancer colorectal cancer diabetes mellitus
A	Pharos: Q9Y5K5	astrocytic tumor lung cancer ovarian cancer hereditary spastic paraplegia non-small cell lung carcinoma psoriasis invasive ductal breast carcinoma oligodendroglioma

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.