4OCM | pdb_00004ocm

Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ib

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody 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)
F	d4ocmf1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
F	d4ocmf3	Artifacts	Tags	Tags	Tags	C-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
F	d4ocmf2	Artifacts	Tags	Tags	Tags	N-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
C	d4ocmc1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
C	d4ocmc3	Artifacts	Tags	Tags	Tags	C-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
C	d4ocmc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
E	d4ocme_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	JAB1/MPN domain	JAB1/MPN domain	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d4ocmb_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	JAB1/MPN domain	JAB1/MPN domain	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
D	d4ocmd_	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	d4ocma_	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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	JAB1/MPN domain-like	8053248	3001105	SCOP2B (2022-06-29)
B	SCOP2 Family	JAB1/Mov34/MPN/PAD-1/JAMM domain-like	8048101	4006292	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	JAB1/MPN domain-like	8053248	3001105	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	JAB1/MPN domain-like	8053272	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)
F	V-set_12	e4ocmF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
C	V-set_12	e4ocmC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
E	JAB	e4ocmE1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: JAB	ECOD (1.6)
B	JAB	e4ocmB1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: JAB	ECOD (1.6)
D	JAB	e4ocmD1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: JAB	ECOD (1.6)
A	JAB	e4ocmA1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: JAB	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
B	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
D	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)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C, F	Heavy Chain	IGHV1	-	26s proteasome regulatory subunit rpn11 \| 26s proteasome regulatory subunit rpn8	SAbDab (2025-12-05)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F	Nb1	-	-	-
B, E	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 peroxisome organization organelle organization peroxisome fission organelle fission mitochondrial fission mitochondrion organization 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 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, D	26S proteasome regulatory subunit RPN8	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process proteasomal protein catabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein 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, E	IPR050242	JAMM/MPN+ metalloenzymes, peptidase M67A	Family
B, E	IPR037518	MPN domain	Domain
B, E	IPR056263	26S proteasome regulatory subunit RPN11, C-terminal domain	Domain
B, E	IPR000555	JAB1/MPN/MOV34 metalloenzyme domain	Domain
A, D	IPR024969	EIF3F/CSN6-like, C-terminal	Domain
A, D	IPR037518	MPN domain	Domain
A, D	IPR033858	26S Proteasome non-ATPase regulatory subunit 7/8	Family
A, D	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.