› 4hrc

X-ray diffraction
2.8Å resolution

Crystal structure of yeast 20S proteasome in complex with epoxyketone carmaphycin analogue 3

Released:
DOI: 10.2210/pdb4hrc/pdb
PDB entry 4hrc coloured by chain, front view.
PDB entry 4hrc coloured by chain, side view.
PDB entry 4hrc coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Enzyme inhibition by hydroamination: design and mechanism of a hybrid carmaphycin-syringolin enone proteasome inhibitor.
Trivella DB, Pereira AR, Stein ML, Kasai Y, Byrum T, Valeriote FA, Tantillo DJ, Groll M, Gerwick WH, Moore BS
Chem Biol 21 782-91 (2014)
PMID: 24930969

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)
Assembly name:
PDBe Complex ID:
PDB-CPX-149135 (preferred)
Entry contents:
14 distinct polypeptide molecules
Macromolecules (14 distinct):
Proteasome subunit alpha type-2 Chains: A, O
Molecule details ›
Chains: A, O
Length: 249 amino acids
Theoretical weight: 27.06 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P23639 (Residues: 2-250; 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: 244 amino acids
Theoretical weight: 27.05 KDa
Source organism: Saccharomyces cerevisiae S288C
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: C, Q
Molecule details ›
Chains: C, Q
Length: 241 amino acids
Theoretical weight: 26.9 KDa
Source organism: Saccharomyces cerevisiae S288C
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: D, R
Molecule details ›
Chains: D, R
Length: 242 amino acids
Theoretical weight: 26.54 KDa
Source organism: Saccharomyces cerevisiae S288C
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: E, S
Molecule details ›
Chains: E, S
Length: 233 amino acids
Theoretical weight: 25.5 KDa
Source organism: Saccharomyces cerevisiae S288C
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: F, T
Molecule details ›
Chains: F, T
Length: 244 amino acids
Theoretical weight: 26.89 KDa
Source organism: Saccharomyces cerevisiae S288C
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 alpha type-1 Chains: G, U
Molecule details ›
Chains: G, U
Length: 243 amino acids
Theoretical weight: 27.32 KDa
Source organism: Saccharomyces cerevisiae S288C
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 beta type-2 Chains: H, V
Molecule details ›
Chains: H, V
Length: 222 amino acids
Theoretical weight: 23.99 KDa
Source organism: Saccharomyces cerevisiae S288C
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: I, W
Molecule details ›
Chains: I, W
Length: 204 amino acids
Theoretical weight: 22.5 KDa
Source organism: Saccharomyces cerevisiae S288C
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: J, X
Molecule details ›
Chains: J, X
Length: 198 amino acids
Theoretical weight: 22.55 KDa
Source organism: 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 Chains: K, Y
Molecule details ›
Chains: K, Y
Length: 212 amino acids
Theoretical weight: 23.33 KDa
Source organism: Saccharomyces cerevisiae S288C
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: L, Z
Molecule details ›
Chains: L, Z
Length: 222 amino acids
Theoretical weight: 24.88 KDa
Source organism: Saccharomyces cerevisiae S288C
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: M, a
Molecule details ›
Chains: M, a
Length: 233 amino acids
Theoretical weight: 25.95 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P30657 (Residues: 34-266; Coverage: 88%)
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
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

1 bound ligand:
Ligand OV2 6 x OV2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21
Unit cell:
a: 135.35Å b: 300.88Å c: 144.25Å
α: 90° β: 112.74° γ: 90°
R-values:
R R work R free
0.212 0.21 0.243

Quick links

Citations

3 review citations

Marine Cyanobacteria: A Source of Lead Compounds and their Clinically-Relevant Molecular Targets.
Tan et al. (2020)
2 more

2 mentions without citation

Novel anti-HIV peptides containing multiple copies of artificially designed heptad repeat motifs.
Shi et al. (2008)
1 more