Annotations: 3J47

Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth R]	RPN7_PSMD6_C	e3j47R1	A: beta barrels	X: LEE-encoded effector EspG N-terminal domain-related	H: 26S proteasome regulatory subunit RPN7 C-terminal helix	T: 26S proteasome regulatory subunit RPN7 C-terminal helix	F: RPN7_PSMD6_C	ECOD (v294.2)
E [auth Q]	RPN6_C_helix	e3j47Q1	A: beta barrels	X: LEE-encoded effector EspG N-terminal domain-related	H: 26S proteasome regulatory subunit RPN6 C-termial helix	T: 26S proteasome regulatory subunit RPN6 C-termial helix	F: RPN6_C_helix	ECOD (v294.2)
D [auth P]	RPN5_C	e3j47P1	A: beta barrels	X: LEE-encoded effector EspG N-terminal domain-related	H: 26S proteasome regulatory subunit RPN5 C-terminal helix	T: 26S proteasome regulatory subunit RPN5 C-terminal helix	F: RPN5_C	ECOD (v294.2)
C [auth O]	Rpn9_C	e3j47O1	A: beta barrels	X: LEE-encoded effector EspG N-terminal domain-related	H: 26S proteasome regulatory subunit RPN9 C-terminal helix	T: 26S proteasome regulatory subunit RPN9 C-terminal helix	F: Rpn9_C	ECOD (v294.2)
B [auth U]	Ribosomal_S30	e3j47U1	A: beta barrels	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: Ribosomal_S30	ECOD (v294.2)
A [auth V]		e3j47V1	A: beta barrels	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F:	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G [auth S]	PF08375	Proteasome regulatory subunit C-terminal (Rpn3_C)	Proteasome regulatory subunit C-terminal	-	Family
F [auth R]	PF21154	26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix (RPN7_PSMD6_C)	26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix	RPN7/PSDM6 are regulatory subunits from the 26S proteasome. This entry represents the C-terminal helix.	Domain
E [auth Q]	PF18503	26S proteasome subunit RPN6 C-terminal helix domain (RPN6_C_helix)	26S proteasome subunit RPN6 C-terminal helix domain	This is the C-terminal helix domain found in RPN6, a component of the 26S proteasome. The C-terminal helices are essential for lid assembly [1, 2].	Domain
D [auth P]	PF18098	26S proteasome regulatory subunit RPN5 C-terminal domain (RPN5_C)	26S proteasome regulatory subunit RPN5 C-terminal domain	This is the C-terminal domain of the 26S proteasome regulatory subunit RPN5 proteins.This helical domain can be found adjacent to Pfam:PF01399. The 26S proteasome is the major ATP-dependent protease in eukaryotes. Three subcomplexes form this degrada ...	This is the C-terminal domain of the 26S proteasome regulatory subunit RPN5 proteins.This helical domain can be found adjacent to Pfam:PF01399. The 26S proteasome is the major ATP-dependent protease in eukaryotes. Three subcomplexes form this degradation machine: the lid, the base, and the core. The helices found at the C terminus of each lid subunit form a helical bundle that directs the ordered self-assembly of the lid subcomplex. This domain which comprises the tail of RPN5 along with the tail of Rpn9, are important for Rpn12 binding to the lid [1].	Domain
C [auth O]	PF18261	Rpn9 C-terminal helix (Rpn9_C)	Rpn9 C-terminal helix	-	Family
B [auth U]	PF13012	Maintenance of mitochondrial structure and function (MitMem_reg)	Maintenance of mitochondrial structure and function	-	Family
A [auth V]	PF23594	26S proteasome regulatory subunit RPN11 C-terminal domain (RPN11_C)	26S proteasome regulatory subunit RPN11 C-terminal domain	This entry represents the C-terminal helical region of 26S proteosomal subunits. This region is involved in forming a helical bundle with other RPN subunits to help with assembly of the proteosome lid [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H [auth T]	26S proteasome regulatory subunit RPN12	-	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 membrane-bounded organelle nucleus intracellular membrane-bounded organelle
G [auth S]	26S proteasome regulatory subunit RPN3	enzyme regulator activity molecular function regulator 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 regulation of biological process regulation of cellular process regulation of protein metabolic process 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 regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process regulation of catabolic process regulation of primary metabolic process regulation of metabolic process regulation of protein catabolic 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
F [auth R]	26S proteasome regulatory subunit RPN7	structural molecule 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 proteasome accessory complex intracellular anatomical structure cellular anatomical structure proteasome regulatory particle proteasome regulatory particle, lid subcomplex membrane-bounded organelle intracellular organelle organelle protein-containing complex catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex proteasome accessory complex intracellular anatomical structure cellular anatomical structure proteasome regulatory particle proteasome regulatory particle, lid subcomplex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
E [auth Q]	26S proteasome regulatory subunit RPN6	structural molecule 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 cellular component organization cellular component biogenesis proteasome assembly 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 cellular component organization cellular component biogenesis proteasome assembly cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis 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
D [auth P]	26S proteasome regulatory subunit RPN5	-	primary metabolic process protein deneddylation protein modification by small protein removal 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 or removal catabolic process proteasomal protein catabolic process protein catabolic process primary metabolic process protein deneddylation protein modification by small protein removal 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 or removal 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 ubiquitin-dependent protein catabolic process	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 organelle nucleus nuclear protein-containing complex COP9 signalosome 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 organelle nucleus nuclear protein-containing complex COP9 signalosome intracellular membrane-bounded organelle cytoplasm proteasome regulatory particle proteasome regulatory particle, lid subcomplex proteasome accessory complex membraneless organelle intracellular membraneless organelle proteasome storage granule
C [auth O]	26S proteasome regulatory subunit RPN9	structural molecule 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 cellular component organization cellular component biogenesis proteasome assembly 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 cellular component organization cellular component biogenesis proteasome assembly cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis 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 cellular anatomical structure intracellular anatomical structure cytoplasm cytosol proteasome regulatory particle proteasome regulatory particle, lid subcomplex proteasome accessory complex intracellular organelle protein-containing complex catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol proteasome regulatory particle proteasome regulatory particle, lid subcomplex proteasome accessory complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle proteasome storage granule membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B [auth U]	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
A [auth V]	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
H [auth T]	IPR000717	Proteasome component (PCI) domain	Domain
H [auth T]	IPR006746	26S proteasome non-ATPase regulatory subunit Rpn12	Family
H [auth T]	IPR033464	CSN8/PSMD8/EIF3K	Domain
G [auth S]	IPR000717	Proteasome component (PCI) domain	Domain
G [auth S]	IPR013586	26S proteasome non-ATPase regulatory subunit 3, C-terminal	Domain
G [auth S]	IPR057985	26S proteasome non-ATPase regulatory subunit 3, N-terminal TPR repeats	Domain
G [auth S]	IPR050756	COP9 signalosome complex subunit 3	Family
G [auth S]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
F [auth R]	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
F [auth R]	IPR019585	26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1	Family
F [auth R]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
F [auth R]	IPR049549	26S proteasome regulatory subunit RPN7/PSMD6, C-terminal helix	Domain
F [auth R]	IPR000717	Proteasome component (PCI) domain	Domain
F [auth R]	IPR045135	26S proteasome regulatory subunit Rpn7, N-terminal	Domain
F [auth R]	IPR019734	Tetratricopeptide repeat	Repeat
E [auth Q]	IPR050871	26S Proteasome and COP9 Signalosome Components	Family
E [auth Q]	IPR040780	6S proteasome subunit Rpn6, C-terminal helix domain	Domain
E [auth Q]	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
E [auth Q]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
E [auth Q]	IPR040773	26S proteasome regulatory subunit Rpn6, N-terminal	Domain
E [auth Q]	IPR000717	Proteasome component (PCI) domain	Domain
D [auth P]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
D [auth P]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
D [auth P]	IPR000717	Proteasome component (PCI) domain	Domain
D [auth P]	IPR040896	26S proteasome regulatory subunit RPN5, C-terminal domain	Domain
D [auth P]	IPR040134	26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4	Family
D [auth P]	IPR054559	PSMD12/CSN4-like, N-terminal	Domain
C [auth O]	IPR054179	PSD13, N-terminal	Domain
C [auth O]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
C [auth O]	IPR035298	26S Proteasome non-ATPase regulatory subunit 13	Family
C [auth O]	IPR000717	Proteasome component (PCI) domain	Domain
C [auth O]	IPR040798	Rpn9, C-terminal helix	Domain
B [auth U]	IPR024969	EIF3F/CSN6-like, C-terminal	Domain
B [auth U]	IPR037518	MPN domain	Domain
B [auth U]	IPR033858	26S Proteasome non-ATPase regulatory subunit 7/8	Family
B [auth U]	IPR000555	JAB1/MPN/MOV34 metalloenzyme domain	Domain
A [auth V]	IPR050242	JAMM/MPN+ metalloenzymes, peptidase M67A	Family
A [auth V]	IPR037518	MPN domain	Domain
A [auth V]	IPR056263	26S proteasome regulatory subunit RPN11, C-terminal domain	Domain
A [auth V]	IPR000555	JAB1/MPN/MOV34 metalloenzyme domain	Domain

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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.

3J47 | pdb_00003j47

Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage