› 1ryp

X-ray diffraction
1.9Å resolution

CRYSTAL STRUCTURE OF THE 20S PROTEASOME FROM YEAST AT 2.4 ANGSTROMS RESOLUTION

Released:
DOI: 10.2210/pdb1ryp/pdb
PDB entry 1ryp coloured by chain, front view.
PDB entry 1ryp coloured by chain, side view.
PDB entry 1ryp coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structure of 20S proteasome from yeast at 2.4 A resolution.
Groll M, Ditzel L, Löwe J, Stock D, Bochtler M, Bartunik HD, Huber R
Nature 386 463-71 (1997)
PMID: 9087403

Function and Biology Details

Reaction catalysed: 
Cleavage of peptide bonds with very broad specificity.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero 28-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149135 (preferred)
Entry contents:
14 distinct polypeptide molecules
Macromolecules (14 distinct):
Proteasome subunit alpha type-1 Chains: A, O
Molecule details ›
Chains: A, O
Length: 243 amino acids
Theoretical weight: 27.32 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P21243 (Residues: 10-252; Coverage: 96%)
Gene names: PRC2, PRS2, SCL1, YGL011C
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-2 Chains: B, P
Molecule details ›
Chains: B, P
Length: 250 amino acids
Theoretical weight: 27.19 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P23639 (Residues: 1-250; Coverage: 100%)
Gene names: PRE8, PRS4, YML092C
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-3 Chains: C, Q
Molecule details ›
Chains: C, Q
Length: 244 amino acids
Theoretical weight: 27.05 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P23638 (Residues: 2-245; Coverage: 95%)
Gene names: PRE9, PRS5, YGR135W
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-4 Chains: D, R
Molecule details ›
Chains: D, R
Length: 241 amino acids
Theoretical weight: 26.9 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40303 (Residues: 3-243; Coverage: 95%)
Gene names: PRE6, YOL038W
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-5 Chains: E, S
Molecule details ›
Chains: E, S
Length: 242 amino acids
Theoretical weight: 26.54 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32379 (Residues: 9-250; Coverage: 93%)
Gene names: DOA5, G9155, PUP2, YGR253C
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-6 Chains: F, T
Molecule details ›
Chains: F, T
Length: 233 amino acids
Theoretical weight: 25.5 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40302 (Residues: 2-234; Coverage: 100%)
Gene names: PRE5, YM9924.06, YMR314W
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Probable proteasome subunit alpha type-7 Chains: G, U
Molecule details ›
Chains: G, U
Length: 244 amino acids
Theoretical weight: 26.89 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P21242 (Residues: 5-248; Coverage: 85%)
Gene names: O6650, PRC1, PRE10, PRS1, YOR362C
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-1 Chains: H, V
Molecule details ›
Chains: H, V
Length: 205 amino acids
Theoretical weight: 22.4 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38624 (Residues: 11-215; Coverage: 95%)
Gene names: J1407, PRE3, YJL001W
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-2 Chains: I, W
Molecule details ›
Chains: I, W
Length: 222 amino acids
Theoretical weight: 23.99 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25043 (Residues: 30-251; Coverage: 85%)
Gene names: PUP1, YOR157C
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-3 Chains: J, X
Molecule details ›
Chains: J, X
Length: 204 amino acids
Theoretical weight: 22.5 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25451 (Residues: 2-205; Coverage: 100%)
Gene names: PUP3, YER094C
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-4 Chains: K, Y
Molecule details ›
Chains: K, Y
Length: 198 amino acids
Theoretical weight: 22.55 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P22141 (Residues: 1-198; Coverage: 100%)
Gene names: PRE1, YER012W
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-5 Chains: L, Z
Molecule details ›
Chains: L, Z
Length: 212 amino acids
Theoretical weight: 23.35 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P30656 (Residues: 76-287; Coverage: 74%)
Gene names: DOA3, P8283.10, PRE2, PRG1, YPR103W
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-6 Chains: 1, M
Molecule details ›
Chains: 1, M
Length: 222 amino acids
Theoretical weight: 24.88 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P23724 (Residues: 20-241; Coverage: 92%)
Gene names: PRE7, PRS3, PTS1, YBL0407, YBL041W
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-7 Chains: 2, N
Molecule details ›
Chains: 2, N
Length: 233 amino acids
Theoretical weight: 25.95 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P30657 (Residues: 34-266; Coverage: 88%)
Gene names: PRE4, YFR050C
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

Ligands and Environments

1 bound ligand:
Ligand MG 20 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MPG/DESY, HAMBURG BEAMLINE BW6
Spacegroup: P21
Unit cell:
a: 135.49Å b: 300.7Å c: 144.42Å
α: 90° β: 112.89° γ: 90°
R-values:
R R work R free
0.286 0.286 0.33

Quick links

Citations

378 review citations

The ubiquitin system.
Hershko et al. (1998)
377 more

53 mentions without citation

Molecular architecture and assembly of the eukaryotic proteasome.
Tomko et al. (2013)
52 more