4O8X | pdb_00004o8x

Zinc-bound Rpn11 in complex with Rpn8

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d4o8xb_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	JAB1/MPN domain	JAB1/MPN domain	Proteasome regulatory subunit Rpn11	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d4o8xa1	Alpha and beta proteins (a/b)	Cytidine deaminase-like	JAB1/MPN domain	JAB1/MPN domain	Proteasome regulatory subunit Rpn8	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d4o8xa2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	JAB1/MPN domain-like	8053248	3001105	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	JAB1/MPN domain-like	8053272	3001105	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)
B	KAsynt_C_assoc	e4o8xB1	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: Type II ABC importer transmembrane domain fold	T: Type II ABC importer transmembrane domain fold	F: KAsynt_C_assoc	ECOD (v294.1)
A	NiFe_hyd_SSU_C	e4o8xA1	A: a/b three-layered sandwiches	X: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	F: NiFe_hyd_SSU_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
A	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01398	JAB1/Mov34/MPN/PAD-1 ubiquitin protease (JAB)	JAB1/Mov34/MPN/PAD-1 ubiquitin protease	Proteins with this domain are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This domain is known as the MPN domain [3] and PAD-1-like domain [4], JABP1 domain [5] or J ...	Proteins with this domain are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This domain is known as the MPN domain [3] and PAD-1-like domain [4], JABP1 domain [5] or JAMM domain [7]. These are metalloenzymes that function as the ubiquitin isopeptidase/ deubiquitinase in the ubiquitin-based signalling and protein turnover pathways in eukaryotes [7]. Versions of the domain in prokaryotic cognates of the ubiquitin-modification pathway are shown to have a similar role, and the archaeal protein from Haloferax volcanii is found to cleave ubiquitin-like small archaeal modifier proteins (SAMP1/2) from protein conjugates [8,9].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	26S proteasome regulatory subunit RPN11	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity cysteine-type peptidase activity ubiquitin-like protein peptidase activity cysteine-type deubiquitinase activity deubiquitinase activity protein-containing complex binding binding proteasome binding cation binding ion binding peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity cysteine-type peptidase activity ubiquitin-like protein peptidase activity cysteine-type deubiquitinase activity deubiquitinase activity protein-containing complex binding binding proteasome binding cation binding ion binding metal ion binding small molecule binding metal-dependent deubiquitinase 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 protein deubiquitination primary metabolic process protein modification by small protein removal macromolecule modification metabolic process protein metabolic 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 protein deubiquitination primary metabolic process protein modification by small protein removal macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal positive regulation of proteasomal protein catabolic process regulation of cellular process catabolic process positive regulation of protein metabolic process positive regulation of biological process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biological process regulation of protein metabolic process biological regulation proteasomal protein catabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of metabolic process regulation of protein catabolic process peroxisome organization organelle organization peroxisome fission organelle fission mitochondrial fission mitochondrion organization organelle assembly membraneless organelle assembly proteasome storage granule assembly	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex cytosol proteasome regulatory particle proteasome regulatory particle, lid subcomplex proteasome accessory complex membraneless organelle intracellular membraneless organelle proteasome storage granule nucleus
A	26S proteasome regulatory subunit RPN8	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity	catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process	protein-containing complex catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex intracellular anatomical structure proteasome regulatory particle proteasome regulatory particle, lid subcomplex proteasome accessory complex cellular anatomical structure intracellular organelle organelle membraneless organelle protein-containing complex catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex intracellular anatomical structure proteasome regulatory particle proteasome regulatory particle, lid subcomplex proteasome accessory complex cellular anatomical structure intracellular organelle organelle membraneless organelle intracellular membraneless organelle cytoplasm proteasome storage granule

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR050242	JAMM/MPN+ metalloenzymes, peptidase M67A	Family
B	IPR037518	MPN domain	Domain
B	IPR056263	26S proteasome regulatory subunit RPN11, C-terminal domain	Domain
B	IPR000555	JAB1/MPN/MOV34 metalloenzyme domain	Domain
A	IPR024969	EIF3F/CSN6-like, C-terminal	Domain
A	IPR037518	MPN domain	Domain
A	IPR033858	26S Proteasome non-ATPase regulatory subunit 7/8	Family
A	IPR000555	JAB1/MPN/MOV34 metalloenzyme domain	Domain

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.