4ADY | pdb_00004ady

Crystal structure of 26S proteasome subunit Rpn2

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
A	d4adya1	All alpha proteins	alpha-alpha superhelix	ARM repeat	Proteasome/cyclosome repeat (PC repeat)	Proteasome regulatory subunit Rpn2, PC domain	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d4adya2	All alpha proteins	alpha-alpha superhelix	Proteasome regulatory subunit Rpn2 N-terminal domain-like	Proteasome regulatory subunit Rpn2, N-terminal domain-like	Proteasome regulatory subunit Rpn2, N-terminal domain	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d4adya3	All beta proteins	Prealbumin-like	Proteasome regulatory subunit Rpn2 C-terminal domain-like	Proteasome regulatory subunit Rpn2, C-terminal domain-like	Proteasome regulatory subunit Rpn2, C-terminal domain	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d4adyb1	All alpha proteins	alpha-alpha superhelix	ARM repeat	Proteasome/cyclosome repeat (PC repeat)	Proteasome regulatory subunit Rpn2, PC domain	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	RPN2_N	e4adyA1	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: 26S proteasome subunit Rpn2 N-terminal domain	T: 26S proteasome subunit Rpn2 N-terminal domain	F: RPN2_N	ECOD (v294.1)
A	PC_rep, HEAT_2	e4adyA2	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: Proteasome/cyclosome (PC) repeat	T: Proteasome/cyclosome (PC) repeat	F: PC_rep, HEAT_2	ECOD (v294.1)
A	LANA1_DNA-bd	e4adyA3	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: Viral DNA-binding domain	T: Viral DNA-binding domain	F: LANA1_DNA-bd	ECOD (v294.1)
B	FANCI_S1-cap,FANCI_S1,FANCI_S2,FANCI_S3,FANCI_S4,FANCI_HD1,FANCI_HD2	e4adyB1	A: a/b three-layered sandwiches	X: barrel domains in phase 1 flagellin	H: Class II aaRS and biotin synthetases	T: Class II aaRS and biotin synthetases	F: FANCI_S1-cap,FANCI_S1,FANCI_S2,FANCI_S3,FANCI_S4,FANCI_HD1,FANCI_HD2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (4.3.0)
B	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF13646	HEAT repeats (HEAT_2)	HEAT repeats	-	Repeat
A, B	PF18004	26S proteasome regulatory subunit RPN2 C-terminal domain (RPN2_C)	26S proteasome regulatory subunit RPN2 C-terminal domain	This is the C-terminal domain found in S. cerevisiae Rpn2 (26S proteasome regulatory subunit RPN2) as well as other eukaryotic species. A study revealed that the C-terminal 52 residues of the Rpn2 C-terminal domain are responsible for mediating inter ...	This is the C-terminal domain found in S. cerevisiae Rpn2 (26S proteasome regulatory subunit RPN2) as well as other eukaryotic species. A study revealed that the C-terminal 52 residues of the Rpn2 C-terminal domain are responsible for mediating interactions with the ubiquitin-binding subunit Rpn13. Futhermore, the extreme C-terminal 20 or 21 residues of Rpn2 (926-945 or 925-945) of S. cerevisiae, were shown to be equally effective at binding Rpn13. Multiple sequence alignments indicate that Rpn2 orthologs are highly conserved in this C-terminal region and share characteristic acidic, aromatic, and proline residues, suggesting a common function. In the structure of Rpn2 from S. cerevisiae , this region is exposed and disordered, and is thus accessible for associating with Rpn13. The Rpn2 binding surface of human Rpn13 has been mapped by nuclear magnetic resonance titration to one surface of its Pru domain [1].	Domain
A, B	PF21505	26S proteasome subunit RPN2, N-terminal domain (RPN2_N)	26S proteasome subunit RPN2, N-terminal domain	-	Repeat
A, B	PF01851	Proteasome/cyclosome repeat (PC_rep)	Proteasome/cyclosome repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	26S PROTEASOME REGULATORY SUBUNIT RPN2	ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding 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 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 accessory complex cellular anatomical structure proteasome regulatory particle, base subcomplex 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 accessory complex cellular anatomical structure proteasome regulatory particle, base subcomplex intracellular organelle organelle membraneless organelle intracellular membraneless organelle cytoplasm proteasome storage granule membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR040623	26S proteasome regulatory subunit RPN2, C-terminal	Domain
A, B	IPR016024	Armadillo-type fold	Homologous Superfamily
A, B	IPR002015	Proteasome/cyclosome repeat	Repeat
A, B	IPR011989	Armadillo-like helical	Homologous Superfamily
A, B	IPR048570	26S proteasome non-ATPase regulatory subunit 1/RPN2, N-terminal domain	Domain
A, B	IPR016642	26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit	Family

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.