1yar

Structure of Archeabacterial 20S proteasome mutant D9S- PA26 complex

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Proteasome alpha subunit

Thermoplasma acidophilum

UniProt P25156

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 42 Proteasome beta subunit × 14 (P28061) proteasome activator protein PA26 × 14 SULFATE ION × 42 GLYCEROL × 14 water × 42 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PSMA_THEAC
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–233; UniProt 1–233 Author chain B; PDBConstruct 1–233; UniProt 1–233 Author chain C; PDBConstruct 1–233; UniProt 1–233 Author chain D; PDBConstruct 1–233; UniProt 1–233 Author chain E; PDBConstruct 1–233; UniProt 1–233 Author chain F; PDBConstruct 1–233; UniProt 1–233 Author chain G; PDBConstruct 1–233; UniProt 1–233

Proteasome beta subunit

Thermoplasma acidophilum

UniProt P28061

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 42 Proteasome alpha subunit × 14 (P25156) proteasome activator protein PA26 × 14 SULFATE ION × 42 GLYCEROL × 14 water × 42 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PSMB_THEAC
Isoform —
PDB entities 2
Chains and sequence ranges Author chain H; PDBConstruct 1–211; UniProt 1–211 Author chain I; PDBConstruct 1–211; UniProt 1–211 Author chain J; PDBConstruct 1–211; UniProt 1–211 Author chain K; PDBConstruct 1–211; UniProt 1–211 Author chain L; PDBConstruct 1–211; UniProt 1–211 Author chain M; PDBConstruct 1–211; UniProt 1–211 Author chain N; PDBConstruct 1–211; UniProt 1–211

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id1yar
Deposition date deposition_date2004-12-17
Structure title titleStructure of Archeabacterial 20S proteasome mutant D9S- PA26 complex
Keywords keywordsproteasome 20S, PA26 proteasome activator 11S, HYDROLASE-HYDROLASE ACTIVATOR COMPLEX; HYDROLASE/HYDROLASE ACTIVATOR
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1yar__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1yar__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 1010 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1yar__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg(Guinier)80.37 Å
Rg (electron density)81.07 Å
Total Rg80.77 Å
Atom count69678
Residues8988
Excluded volume1248000 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1yar__assembly_1__model_1 42-meric (42) Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

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6. Fold Classification (SCOP + CATH) 42 domains

SCOP 2.08 (21 domains)

Domain ID domain_idd1yara_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.153 — Ntn hydrolase-like
Superfamily Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family familyd.153.1.4 — Proteasome subunits
Domain ID domain_idd1yarb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.153 — Ntn hydrolase-like
Superfamily Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family familyd.153.1.4 — Proteasome subunits
Domain ID domain_idd1yarc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.153 — Ntn hydrolase-like
Superfamily Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family familyd.153.1.4 — Proteasome subunits
Domain ID domain_idd1yard_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.153 — Ntn hydrolase-like
Superfamily Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family familyd.153.1.4 — Proteasome subunits
Domain ID domain_idd1yare_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.153 — Ntn hydrolase-like
Superfamily Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family familyd.153.1.4 — Proteasome subunits
Domain ID domain_idd1yarf_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.153 — Ntn hydrolase-like
Superfamily Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family familyd.153.1.4 — Proteasome subunits
Domain ID domain_idd1yarg_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.153 — Ntn hydrolase-like
Superfamily Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family familyd.153.1.4 — Proteasome subunits
Domain ID domain_idd1yarh_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.153 — Ntn hydrolase-like
Superfamily Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family familyd.153.1.4 — Proteasome subunits
Domain ID domain_idd1yari_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.153 — Ntn hydrolase-like
Superfamily Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family familyd.153.1.4 — Proteasome subunits
Domain ID domain_idd1yarj_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.153 — Ntn hydrolase-like
Superfamily Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family familyd.153.1.4 — Proteasome subunits
Domain ID domain_idd1yark_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.153 — Ntn hydrolase-like
Superfamily Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family familyd.153.1.4 — Proteasome subunits
Domain ID domain_idd1yarl_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.153 — Ntn hydrolase-like
Superfamily Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family familyd.153.1.4 — Proteasome subunits
Domain ID domain_idd1yarm_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.153 — Ntn hydrolase-like
Superfamily Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family familyd.153.1.4 — Proteasome subunits
Domain ID domain_idd1yarn_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.153 — Ntn hydrolase-like
Superfamily Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family familyd.153.1.4 — Proteasome subunits
Domain ID domain_idd1yaro_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.8 — Proteasome activator
Family Family familya.24.8.1 — Proteasome activator
Domain ID domain_idd1yarp_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.8 — Proteasome activator
Family Family familya.24.8.1 — Proteasome activator
Domain ID domain_idd1yarq_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.8 — Proteasome activator
Family Family familya.24.8.1 — Proteasome activator
Domain ID domain_idd1yarr_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.8 — Proteasome activator
Family Family familya.24.8.1 — Proteasome activator
Domain ID domain_idd1yars_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.8 — Proteasome activator
Family Family familya.24.8.1 — Proteasome activator
Domain ID domain_idd1yart_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.8 — Proteasome activator
Family Family familya.24.8.1 — Proteasome activator
Domain ID domain_idd1yaru_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.8 — Proteasome activator
Family Family familya.24.8.1 — Proteasome activator

CATH v4.4 (21 domains)

Domain ID domain_id1yarA00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
Domain ID domain_id1yarB00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
Domain ID domain_id1yarC00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
Domain ID domain_id1yarD00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
Domain ID domain_id1yarE00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
Domain ID domain_id1yarF00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
Domain ID domain_id1yarG00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
Domain ID domain_id1yarH00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
Domain ID domain_id1yarI00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
Domain ID domain_id1yarJ00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
Domain ID domain_id1yarK00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
Domain ID domain_id1yarL00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
Domain ID domain_id1yarM00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
Domain ID domain_id1yarN00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
Domain ID domain_id1yarO01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily180 — Proteasome activator pa28, C-terminal domain
Domain ID domain_id1yarP01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily180 — Proteasome activator pa28, C-terminal domain
Domain ID domain_id1yarQ01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily180 — Proteasome activator pa28, C-terminal domain
Domain ID domain_id1yarR01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily180 — Proteasome activator pa28, C-terminal domain
Domain ID domain_id1yarS01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily180 — Proteasome activator pa28, C-terminal domain
Domain ID domain_id1yarT01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily180 — Proteasome activator pa28, C-terminal domain
Domain ID domain_id1yarU01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily180 — Proteasome activator pa28, C-terminal domain
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7. Citations (1)