1YAR | pdb_00001yar

Structure of Archeabacterial 20S proteasome mutant D9S- PA26 complex

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)
U	d1yaru_	All alpha proteins	Four-helical up-and-down bundle	Proteasome activator	Proteasome activator	automated matches	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)
T	d1yart_	All alpha proteins	Four-helical up-and-down bundle	Proteasome activator	Proteasome activator	automated matches	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)
S	d1yars_	All alpha proteins	Four-helical up-and-down bundle	Proteasome activator	Proteasome activator	automated matches	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)
R	d1yarr_	All alpha proteins	Four-helical up-and-down bundle	Proteasome activator	Proteasome activator	automated matches	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)
Q	d1yarq_	All alpha proteins	Four-helical up-and-down bundle	Proteasome activator	Proteasome activator	automated matches	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)
P	d1yarp_	All alpha proteins	Four-helical up-and-down bundle	Proteasome activator	Proteasome activator	automated matches	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)
O	d1yaro_	All alpha proteins	Four-helical up-and-down bundle	Proteasome activator	Proteasome activator	automated matches	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)
N	d1yarn_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Thermoplasma acidophilum ) [TaxId: 2303 ],	SCOPe (2.08)
M	d1yarm_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Thermoplasma acidophilum ) [TaxId: 2303 ],	SCOPe (2.08)
L	d1yarl_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Thermoplasma acidophilum ) [TaxId: 2303 ],	SCOPe (2.08)
K	d1yark_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Thermoplasma acidophilum ) [TaxId: 2303 ],	SCOPe (2.08)
J	d1yarj_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Thermoplasma acidophilum ) [TaxId: 2303 ],	SCOPe (2.08)
I	d1yari_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Thermoplasma acidophilum ) [TaxId: 2303 ],	SCOPe (2.08)
H	d1yarh_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Thermoplasma acidophilum ) [TaxId: 2303 ],	SCOPe (2.08)
G	d1yarg_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Thermoplasma acidophilum ) [TaxId: 2303 ],	SCOPe (2.08)
F	d1yarf_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Thermoplasma acidophilum ) [TaxId: 2303 ],	SCOPe (2.08)
E	d1yare_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Thermoplasma acidophilum ) [TaxId: 2303 ],	SCOPe (2.08)
D	d1yard_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Thermoplasma acidophilum ) [TaxId: 2303 ],	SCOPe (2.08)
C	d1yarc_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Thermoplasma acidophilum ) [TaxId: 2303 ],	SCOPe (2.08)
B	d1yarb_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Thermoplasma acidophilum ) [TaxId: 2303 ],	SCOPe (2.08)
A	d1yara_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	automated matches	(Thermoplasma acidophilum ) [TaxId: 2303 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
U	SCOP2B Superfamily	Proteasome activator-like	8032475	3001611	SCOP2B (2022-06-29)
T	SCOP2B Superfamily	Proteasome activator-like	8032475	3001611	SCOP2B (2022-06-29)
S	SCOP2B Superfamily	Proteasome activator-like	8032475	3001611	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	Proteasome activator-like	8032475	3001611	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Proteasome activator-like	8032475	3001611	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Proteasome activator-like	8032475	3001611	SCOP2B (2022-06-29)
O	SCOP2 Family	Proteasome activator	8020095	4000831	SCOP2 (2022-06-29)
O	SCOP2 Superfamily	Proteasome activator-like	8032475	3001611	SCOP2 (2022-06-29)
N	SCOP2B Superfamily	Class II glutamine amidotransferases	8034254	3000131	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Class II glutamine amidotransferases	8034254	3000131	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Class II glutamine amidotransferases	8034254	3000131	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Class II glutamine amidotransferases	8034254	3000131	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Class II glutamine amidotransferases	8034254	3000131	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Class II glutamine amidotransferases	8034254	3000131	SCOP2B (2022-06-29)
H	SCOP2 Family	Proteasome subunits	8021874	4002254	SCOP2 (2022-06-29)
H	SCOP2 Superfamily	Class II glutamine amidotransferases	8034254	3000131	SCOP2 (2022-06-29)
G	SCOP2B Superfamily	Class II glutamine amidotransferases	8034248	3000131	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Class II glutamine amidotransferases	8034248	3000131	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Class II glutamine amidotransferases	8034248	3000131	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Class II glutamine amidotransferases	8034248	3000131	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Class II glutamine amidotransferases	8034248	3000131	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Class II glutamine amidotransferases	8034248	3000131	SCOP2B (2022-06-29)
A	SCOP2 Family	Proteasome subunits	8021868	4002254	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Class II glutamine amidotransferases	8034248	3000131	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
U		e1yarU1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (v294.1)
T		e1yarT1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (v294.1)
S		e1yarS1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (v294.1)
R		e1yarR1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (v294.1)
Q		e1yarQ1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (v294.1)
P		e1yarP1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (v294.1)
O	PA28_C	e1yarO1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Proteasome activator reg(alpha)	T: Proteasome activator reg(alpha)	F: PA28_C	ECOD (v294.1)
N	CBAH	e1yarN1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: CBAH	ECOD (v294.1)
M	CBAH	e1yarM1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: CBAH	ECOD (v294.1)
L	CBAH	e1yarL1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: CBAH	ECOD (v294.1)
K	CBAH	e1yarK1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: CBAH	ECOD (v294.1)
J	CBAH	e1yarJ1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: CBAH	ECOD (v294.1)
I	CBAH	e1yarI1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: CBAH	ECOD (v294.1)
H	Proteasome	e1yarH1	A: few secondary structure elements	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: Proteasome	ECOD (v294.1)
G	CBAH	e1yarG1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: CBAH	ECOD (v294.1)
F	CBAH	e1yarF1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: CBAH	ECOD (v294.1)
E	CBAH	e1yarE1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: CBAH	ECOD (v294.1)
D	CBAH	e1yarD1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: CBAH	ECOD (v294.1)
C	CBAH	e1yarC1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: CBAH	ECOD (v294.1)
B	CBAH	e1yarB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: CBAH	ECOD (v294.1)
A	Proteasome	e1yarA1	A: few secondary structure elements	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: Proteasome	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
U	1.20.120.180	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Proteasome activator pa28, C-terminal domain	CATH (4.3.0)
T	1.20.120.180	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Proteasome activator pa28, C-terminal domain	CATH (4.3.0)
S	1.20.120.180	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Proteasome activator pa28, C-terminal domain	CATH (4.3.0)
R	1.20.120.180	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Proteasome activator pa28, C-terminal domain	CATH (4.3.0)
Q	1.20.120.180	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Proteasome activator pa28, C-terminal domain	CATH (4.3.0)
P	1.20.120.180	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Proteasome activator pa28, C-terminal domain	CATH (4.3.0)
O	1.20.120.180	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Proteasome activator pa28, C-terminal domain	CATH (4.3.0)
N	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
M	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
L	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
K	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
J	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
I	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
H	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
G	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
F	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
E	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
D	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
C	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
B	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
A	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G	PF00227	Proteasome subunit (Proteasome)	Proteasome subunit	The proteasome is a multisubunit structure that degrades proteins. Protein degradation is an essential component of regulation because proteins can become misfolded, damaged, or unnecessary. Proteasomes and their homologues vary greatly in complexity ...	The proteasome is a multisubunit structure that degrades proteins. Protein degradation is an essential component of regulation because proteins can become misfolded, damaged, or unnecessary. Proteasomes and their homologues vary greatly in complexity: from HslV (heat shock locus v), which is encoded by 1 gene in bacteria, to the eukaryotic 20S proteasome, which is encoded by more than 14 genes [1]. Recently evidence of two novel groups of bacterial proteasomes was proposed. The first is Anbu, which is sparsely distributed among cyanobacteria and proteobacteria [1]. The second is call beta-proteobacteria proteasome homologue (BPH) [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
O, P, Q, R, S O, P, Q, R, S, T, U	proteasome activator protein PA26	-	regulation of biological process regulation of cellular process catabolic process regulation of protein metabolic process biological regulation primary metabolic process proteasomal protein catabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process macromolecule catabolic process regulation of primary metabolic process regulation of proteasomal protein catabolic process metabolic process regulation of biological process regulation of cellular process catabolic process regulation of protein metabolic process biological regulation primary metabolic process proteasomal protein catabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process macromolecule catabolic process regulation of primary metabolic process regulation of proteasomal protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process proteolysis	proteasome accessory complex protein-containing complex intracellular anatomical structure cellular anatomical structure catalytic complex peptidase complex proteasome activator complex proteasome complex endopeptidase complex intracellular protein-containing complex
H, I, J, K, L H, I, J, K, L, M, N	Proteasome beta subunit	peptidase activity catalytic activity, acting on a protein threonine-type peptidase activity hydrolase activity catalytic activity endopeptidase activity threonine-type endopeptidase activity	catabolic process proteasomal protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process	protein-containing complex intracellular anatomical structure cellular anatomical structure catalytic complex peptidase complex proteasome complex endopeptidase complex proteasome core complex intracellular protein-containing complex proteasome core complex, beta-subunit complex cytoplasm
A, B, C, D, E A, B, C, D, E, F, G	Proteasome alpha subunit	peptidase activity catalytic activity, acting on a protein threonine-type peptidase activity hydrolase activity catalytic activity endopeptidase activity threonine-type endopeptidase 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	cellular anatomical structure intracellular anatomical structure cytoplasm protein-containing complex proteasome core complex, alpha-subunit complex catalytic complex peptidase complex proteasome complex endopeptidase complex proteasome core complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
O, P, Q, R, S O, P, Q, R, S, T, U	IPR003186	Proteasome activator PA28, C-terminal domain	Domain
O, P, Q, R, S O, P, Q, R, S, T, U	IPR036252	Proteasome activator superfamily	Homologous Superfamily
O, P, Q, R, S O, P, Q, R, S, T, U	IPR036997	Proteasome activator PA28, C-terminal domain superfamily	Homologous Superfamily
H, I, J, K, L H, I, J, K, L, M, N	IPR016050	Proteasome beta-type subunit, conserved site	Conserved Site
H, I, J, K, L H, I, J, K, L, M, N	IPR023333	Proteasome B-type subunit	Family
H, I, J, K, L H, I, J, K, L, M, N	IPR029055	Nucleophile aminohydrolases, N-terminal	Homologous Superfamily
H, I, J, K, L H, I, J, K, L, M, N	IPR019983	Peptidase T1A, proteasome beta-subunit, archaeal	Family
H, I, J, K, L H, I, J, K, L, M, N	IPR001353	Proteasome, subunit alpha/beta	Family
H, I, J, K, L H, I, J, K, L, M, N	IPR000243	Peptidase T1A, proteasome beta-subunit	Family
A, B, C, D, E A, B, C, D, E, F, G	IPR000426	Proteasome alpha-subunit, N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR029055	Nucleophile aminohydrolases, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR050115	Proteasome subunit alpha	Family
A, B, C, D, E A, B, C, D, E, F, G	IPR023332	Proteasome alpha-type subunit	Family
A, B, C, D, E A, B, C, D, E, F, G	IPR001353	Proteasome, subunit alpha/beta	Family
A, B, C, D, E A, B, C, D, E, F, G	IPR019982	Proteasome alpha subunit, archaeal	Family