› 5vfo

Electron Microscopy
3.5Å resolution

Nucleotide-driven Triple-state Remodeling of the AAA-ATPase Channel in the Activated Human 26S Proteasome

Released:
DOI: 10.2210/pdb5vfo/pdb
PDB entry 5vfo coloured by chain, front view.
PDB entry 5vfo coloured by chain, side view.
PDB entry 5vfo coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome.
Zhu Y, Wang WL, Yu D, Ouyang Q, Lu Y, Mao Y
Nat Commun 9 1360 (2018)
PMID: 29636472
Related structures: EMD-8662

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-6 Chains: G, g
Molecule details ›
Chains: G, g
Length: 240 amino acids
Theoretical weight: 26.73 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P60900 (Residues: 5-244; Coverage: 98%)
Gene names: PROS27, PSMA6
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-2 Chains: H, h
Molecule details ›
Chains: H, h
Length: 232 amino acids
Theoretical weight: 25.73 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P25787 (Residues: 3-234; Coverage: 99%)
Gene names: HC3, PSC3, PSMA2
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-4 Chains: I, i
Molecule details ›
Chains: I, i
Length: 250 amino acids
Theoretical weight: 28.12 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P25789 (Residues: 2-251; Coverage: 96%)
Gene names: HC9, PSC9, PSMA4
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-7 Chains: J, j
Molecule details ›
Chains: J, j
Length: 243 amino acids
Theoretical weight: 27.38 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O14818 (Residues: 2-244; Coverage: 98%)
Gene names: HSPC, PSMA7
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-5 Chains: K, k
Molecule details ›
Chains: K, k
Length: 234 amino acids
Theoretical weight: 25.57 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P28066 (Residues: 8-241; Coverage: 97%)
Gene name: PSMA5
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-1 Chains: L, l
Molecule details ›
Chains: L, l
Length: 238 amino acids
Theoretical weight: 26.73 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P25786 (Residues: 4-241; Coverage: 91%)
Gene names: HC2, NU, PROS30, PSC2, PSMA1
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-3 Chains: M, m
Molecule details ›
Chains: M, m
Length: 245 amino acids
Theoretical weight: 27.29 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P25788 (Residues: 2-246; Coverage: 96%)
Gene names: HC8, PSC8, PSMA3
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-6 Chains: N, n
Molecule details ›
Chains: N, n
Length: 191 amino acids
Theoretical weight: 20.47 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P28072 (Residues: 35-225; Coverage: 80%)
Gene names: LMPY, PSMB6, Y
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-7 Chains: O, o
Molecule details ›
Chains: O, o
Length: 220 amino acids
Theoretical weight: 23.75 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q99436 (Residues: 44-263; Coverage: 79%)
Gene names: PSMB7, Z
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-3 Chains: P, p
Molecule details ›
Chains: P, p
Length: 204 amino acids
Theoretical weight: 22.84 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P49720 (Residues: 2-205; Coverage: 100%)
Gene name: PSMB3
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-2 Chains: Q, q
Molecule details ›
Chains: Q, q
Length: 199 amino acids
Theoretical weight: 22.72 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P49721 (Residues: 1-199; Coverage: 99%)
Gene name: PSMB2
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-5 Chains: R, r
Molecule details ›
Chains: R, r
Length: 201 amino acids
Theoretical weight: 22.2 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P28074 (Residues: 60-260; Coverage: 76%)
Gene names: LMPX, MB1, PSMB5, X
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-1 Chains: S, s
Molecule details ›
Chains: S, s
Length: 213 amino acids
Theoretical weight: 23.58 KDa
Source organism: Homo sapiens
Expression system: 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: T, t
Molecule details ›
Chains: T, t
Length: 215 amino acids
Theoretical weight: 23.99 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P28070 (Residues: 46-260; Coverage: 81%)
Gene names: PROS26, PSMB4
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.5Å
Relevant EMDB volumes: EMD-8662
Expression system: Homo sapiens

Quick links

Citations

14 review citations

Structure, Dynamics and Function of the 26S Proteasome.
Mao Y. (2021)
13 more

4 mentions without citation

Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome.
Zhu et al. (2018)
3 more