› 6avo

Electron Microscopy
3.8Å resolution

Cryo-EM structure of human immunoproteasome with a novel noncompetitive inhibitor that selectively inhibits activated lymphocytes

Released:
DOI: 10.2210/pdb6avo/pdb
PDB entry 6avo coloured by chain, front view.
PDB entry 6avo coloured by chain, side view.
PDB entry 6avo coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of human immunoproteasome with a reversible and noncompetitive inhibitor that selectively inhibits activated lymphocytes.
Santos RLA, Bai L, Singh PK, Murakami N, Fan H, Zhan W, Zhu Y, Jiang X, Zhang K, Assker JP, Nathan CF, Li H, Azzi J, Lin G
Nat Commun 8 1692 (2017)
PMID: 29167449
Related structures: EMD-7010

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-127163 (preferred)
Entry contents:
14 distinct polypeptide molecules
Macromolecules (14 distinct):
Proteasome subunit beta type-9 Chains: A, F
Molecule details ›
Chains: A, F
Length: 199 amino acids
Theoretical weight: 21.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P28065 (Residues: 21-219; Coverage: 91%)
Gene names: LMP2, PSMB6i, PSMB9, RING12
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-10 Chains: B, E
Molecule details ›
Chains: B, E
Length: 234 amino acids
Theoretical weight: 24.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P40306 (Residues: 40-273; Coverage: 86%)
Gene names: LMP10, MECL1, PSMB10
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-8 Chains: C, D
Molecule details ›
Chains: C, D
Length: 204 amino acids
Theoretical weight: 22.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P28062 (Residues: 73-276; Coverage: 74%)
Gene names: LMP7, PSMB5i, PSMB8, RING10, Y2
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-1 Chains: G, L
Molecule details ›
Chains: G, L
Length: 263 amino acids
Theoretical weight: 29.6 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-5 Chains: H, M
Molecule details ›
Chains: H, M
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-7 Chains: I, N
Molecule details ›
Chains: I, N
Length: 248 amino acids
Theoretical weight: 27.93 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-3 Chains: J, Q
Molecule details ›
Chains: J, Q
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: K, R
Molecule details ›
Chains: K, R
Length: 246 amino acids
Theoretical weight: 27.43 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 alpha type-4 Chains: O, Z
Molecule details ›
Chains: O, Z
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-2 Chains: P, b
Molecule details ›
Chains: P, b
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 beta type-1 Chains: S, X
Molecule details ›
Chains: S, X
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-2 Chains: T, V
Molecule details ›
Chains: T, V
Length: 201 amino acids
Theoretical weight: 22.86 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-3 Chains: U, Y
Molecule details ›
Chains: U, Y
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-4 Chains: W, a
Molecule details ›
Chains: W, 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

Ligands and Environments

1 bound ligand:
Ligand BZ7 2 x BZ7
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-7010

Quick links

Citations

12 review citations

The immunoproteasome and thymoproteasome: functions, evolution and human disease.
Murata et al. (2018)
11 more

2 mentions without citation

Structure of human immunoproteasome with a reversible and noncompetitive inhibitor that selectively inhibits activated lymphocytes.
Santos et al. (2017)
1 more