› 5l5i

X-ray diffraction
2.9Å resolution

Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 9

Released:
DOI: 10.2210/pdb5l5i/pdb
PDB entry 5l5i coloured by chain, front view.
PDB entry 5l5i coloured by chain, side view.
PDB entry 5l5i coloured by chain, top view.
Source organisms:
Primary publication:
A humanized yeast proteasome identifies unique binding modes of inhibitors for the immunosubunit β5i.
Huber EM, Heinemeyer W, de Bruin G, Overkleeft HS, Groll M
EMBO J 35 2602-2613 (2016)
PMID: 27789522

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 28-mer (preferred)
PDBe Complex ID:
PDB-CPX-149017 (preferred)
Entry contents:
14 distinct polypeptide molecules
Macromolecules (14 distinct):
Proteasome subunit alpha type-2 Chains: A, O
Molecule details ›
Chains: A, O
Length: 250 amino acids
Theoretical weight: 27.19 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
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: B, P
Molecule details ›
Chains: B, P
Length: 258 amino acids
Theoretical weight: 28.75 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P23638 (Residues: 1-258; Coverage: 100%)
Gene names: PRE9, PRS5, YGR135W
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-4 Chains: C, Q
Molecule details ›
Chains: C, Q
Length: 254 amino acids
Theoretical weight: 28.48 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40303 (Residues: 1-254; Coverage: 100%)
Gene names: PRE6, YOL038W
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-5 Chains: D, R
Molecule details ›
Chains: D, R
Length: 260 amino acids
Theoretical weight: 28.65 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32379 (Residues: 1-260; Coverage: 100%)
Gene names: DOA5, G9155, PUP2, YGR253C
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-6 Chains: E, S
Molecule details ›
Chains: E, S
Length: 234 amino acids
Theoretical weight: 25.63 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40302 (Residues: 1-234; 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: F, T
Molecule details ›
Chains: F, T
Length: 288 amino acids
Theoretical weight: 31.58 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P21242 (Residues: 1-288; Coverage: 100%)
Gene names: O6650, PRC1, PRE10, PRS1, YOR362C
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-1 Chains: G, U
Molecule details ›
Chains: G, U
Length: 252 amino acids
Theoretical weight: 28.03 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P21243 (Residues: 1-252; Coverage: 100%)
Gene names: PRC2, PRS2, SCL1, YGL011C
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-2 Chains: H, V
Molecule details ›
Chains: H, V
Length: 232 amino acids
Theoretical weight: 25.11 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25043 (Residues: 30-261; Coverage: 89%)
Gene names: PUP1, YOR157C
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-3 Chains: I, W
Molecule details ›
Chains: I, W
Length: 205 amino acids
Theoretical weight: 22.63 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25451 (Residues: 1-205; Coverage: 100%)
Gene names: PUP3, YER094C
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-4 Chains: J, X
Molecule details ›
Chains: J, X
Length: 198 amino acids
Theoretical weight: 22.55 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
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; Proteasome subunit beta type-8 Chains: K, Y
Molecule details ›
Chains: K, Y
Length: 211 amino acids
Theoretical weight: 23.36 KDa
Source organisms: Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P28062 (Residues: 73-210; Coverage: 50%)
  • Canonical: P30656 (Residues: 215-287; Coverage: 25%)
Gene names: DOA3, LMP7, P8283.10, PRE2, PRG1, PSMB5i, PSMB8, RING10, Y2, YPR103W
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-1; Proteasome subunit beta type-6 Chains: L, Z
Molecule details ›
Chains: L, Z
Length: 222 amino acids
Theoretical weight: 24.98 KDa
Source organisms: Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P23724 (Residues: 20-117, 131-150, 153-241; Coverage: 86%)
  • Canonical: P20618 (Residues: 126-138, 159-160; Coverage: 6%)
Gene names: PRE7, PRS3, PSC5, PSMB1, PTS1, YBL0407, YBL041W
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-7 Chains: M, a
Molecule details ›
Chains: M, a
Length: 246 amino acids
Theoretical weight: 27.2 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P30657 (Residues: 21-266; Coverage: 93%)
Gene names: PRE4, YFR050C
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-1 Chains: N, b
Molecule details ›
Chains: N, b
Length: 196 amino acids
Theoretical weight: 21.52 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38624 (Residues: 20-215; Coverage: 91%)
Gene names: J1407, PRE3, YJL001W
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

Ligands and Environments

4 bound ligands:
Ligand MG 8 x MG
Ligand CL 2 x CL
Ligand 38X 2 x 38X
Ligand MES 2 x MES
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21
Unit cell:
a: 135.71Å b: 299.42Å c: 145.97Å
α: 90° β: 112.82° γ: 90°
R-values:
R R work R free
0.178 0.176 0.21
Expression system: Saccharomyces cerevisiae S288C

Quick links

Citations

2 review citations

Site-Specific Proteasome Inhibitors.
Kisselev AF. (2021)
1 more