› 5le5

X-ray diffraction
1.8Å resolution

Native human 20S proteasome at 1.8 Angstrom

Released:
DOI: 10.2210/pdb5le5/pdb
PDB entry 5le5 coloured by chain, front view.
PDB entry 5le5 coloured by chain, side view.
PDB entry 5le5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The inhibition mechanism of human 20S proteasomes enables next-generation inhibitor design.
Schrader J, Henneberg F, Mata RA, Tittmann K, Schneider TR, Stark H, Bourenkov G, Chari A
Science 353 594-8 (2016)
PMID: 27493187

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-127173 (preferred)
Entry contents:
14 distinct polypeptide molecules
Macromolecules (14 distinct):
Proteasome subunit alpha type-2 Chains: A, O
Molecule details ›
Chains: A, O
Length: 234 amino acids
Theoretical weight: 25.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25787 (Residues: 1-234; Coverage: 100%)
Gene names: HC3, PSC3, PSMA2
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-4 Chains: B, P
Molecule details ›
Chains: B, P
Length: 261 amino acids
Theoretical weight: 29.53 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25789 (Residues: 1-261; Coverage: 100%)
Gene names: HC9, PSC9, PSMA4
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-7 Chains: C, Q
Molecule details ›
Chains: C, Q
Length: 248 amino acids
Theoretical weight: 27.99 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O14818 (Residues: 1-248; Coverage: 100%)
Gene names: HSPC, PSMA7
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-5 Chains: D, R
Molecule details ›
Chains: D, R
Length: 241 amino acids
Theoretical weight: 26.44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P28066 (Residues: 1-241; Coverage: 100%)
Gene name: PSMA5
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-1 Chains: E, S
Molecule details ›
Chains: E, S
Length: 263 amino acids
Theoretical weight: 29.72 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25786 (Residues: 1-263; Coverage: 100%)
Gene names: HC2, NU, PROS30, PSC2, PSMA1
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-3 Chains: F, T
Molecule details ›
Chains: F, T
Length: 255 amino acids
Theoretical weight: 28.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25788 (Residues: 1-255; Coverage: 100%)
Gene names: HC8, PSC8, PSMA3
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-6 Chains: G, U
Molecule details ›
Chains: G, U
Length: 246 amino acids
Theoretical weight: 27.74 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P60900 (Residues: 1-246; Coverage: 100%)
Gene names: PROS27, PSMA6
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-7 Chains: H, V
Molecule details ›
Chains: H, V
Length: 234 amino acids
Theoretical weight: 25.32 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q99436 (Residues: 44-277; Coverage: 85%)
Gene names: PSMB7, Z
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: 22.97 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P49720 (Residues: 1-205; Coverage: 100%)
Gene name: PSMB3
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-2 Chains: J, X
Molecule details ›
Chains: J, X
Length: 201 amino acids
Theoretical weight: 22.99 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P49721 (Residues: 1-201; Coverage: 100%)
Gene name: PSMB2
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: 204 amino acids
Theoretical weight: 22.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P28074 (Residues: 60-263; Coverage: 78%)
Gene names: LMPX, MB1, PSMB5, X
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-1 Chains: L, Z
Molecule details ›
Chains: L, Z
Length: 213 amino acids
Theoretical weight: 23.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P20618 (Residues: 29-241; Coverage: 88%)
Gene names: PSC5, PSMB1
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-4 Chains: M, a
Molecule details ›
Chains: M, a
Length: 219 amino acids
Theoretical weight: 24.41 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P28070 (Residues: 46-264; Coverage: 83%)
Gene names: PROS26, PSMB4
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-6 Chains: N, b
Molecule details ›
Chains: N, b
Length: 205 amino acids
Theoretical weight: 21.92 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P28072 (Residues: 35-239; Coverage: 86%)
Gene names: LMPY, PSMB6, Y
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

Ligands and Environments

4 bound ligands:
Ligand CL 57 x CL
Ligand 1PE 9 x 1PE
Ligand K 6 x K
Ligand MG 10 x MG
2 modified residues:
Ligand YCM 4 x YCM
Ligand 6V1 8 x 6V1

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)
Spacegroup: P212121
Unit cell:
a: 113.44Å b: 202.77Å c: 316Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.182 0.212

Quick links

Citations

21 review citations

The versatility of boron in biological target engagement.
Diaz et al. (2017)
20 more

16 mentions without citation

Revisiting Proteasome Inhibitors: Molecular Underpinnings of Their Development, Mechanisms of Resistance and Strategies to Overcome Anti-Cancer Drug Resistance.
Leonardo-Sousa et al. (2022)
15 more