› 3jck

Electron Microscopy
3.5Å resolution

Structure of the yeast 26S proteasome lid sub-complex

Released:
DOI: 10.2210/pdb3jck/pdb
PDB entry 3jck coloured by chain, ensemble of 5 models, front view.
PDB entry 3jck coloured by chain, ensemble of 5 models, side view.
PDB entry 3jck coloured by chain, ensemble of 5 models, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition.
Dambacher CM, Worden EJ, Herzik MA, Martin A, Lander GC
Elife 5 e13027 (2016)
PMID: 26744777
Related structures: EMD-6479

Function and Biology Details

Reaction catalysed: 
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero nonamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131727 (preferred)
Entry contents:
9 distinct polypeptide molecules
Macromolecules (9 distinct):
26S proteasome regulatory subunit RPN3 Chain: A
Molecule details ›
Chain: A
Length: 438 amino acids
Theoretical weight: 49.57 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P40016 (Residues: 131-523; Coverage: 75%)
Gene names: RPN3, SUN2, YER021W
Sequence domains:
26S proteasome regulatory subunit RPN5 Chain: B
Molecule details ›
Chain: B
Length: 445 amino acids
Theoretical weight: 51.84 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q12250 (Residues: 1-445; Coverage: 100%)
Gene names: D1572, NAS5, RPN5, YDL147W
Sequence domains:
26S proteasome regulatory subunit RPN6 Chain: C
Molecule details ›
Chain: C
Length: 434 amino acids
Theoretical weight: 49.84 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q12377 (Residues: 1-434; Coverage: 100%)
Gene names: D2381, NAS4, RPN6, YDL097C
Sequence domains:
Structure domains: Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
26S proteasome regulatory subunit RPN7 Chain: D
Molecule details ›
Chain: D
Length: 429 amino acids
Theoretical weight: 49.02 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q06103 (Residues: 1-429; Coverage: 100%)
Gene names: P8283.8, RPN7, YPR108W
Sequence domains:
26S proteasome regulatory subunit RPN8 Chain: E
Molecule details ›
Chain: E
Length: 338 amino acids
Theoretical weight: 38.37 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q08723 (Residues: 1-338; Coverage: 100%)
Gene names: O5360, RPN8, YOR261C
Sequence domains:
26S proteasome regulatory subunit RPN9 Chain: F
Molecule details ›
Chain: F
Length: 393 amino acids
Theoretical weight: 45.84 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q04062 (Residues: 1-393; Coverage: 100%)
Gene names: D9461.14, NAS7, RPN9, YDR427W
Sequence domains:
Ubiquitin carboxyl-terminal hydrolase RPN11 Chain: G
Molecule details ›
Chain: G
Length: 306 amino acids
Theoretical weight: 34.44 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P43588 (Residues: 1-306; Coverage: 100%)
Gene names: MPR1, RPN11, YFR004W
Sequence domains: JAB1/Mov34/MPN/PAD-1 ubiquitin protease
26S proteasome regulatory subunit RPN12 Chain: H
Molecule details ›
Chain: H
Length: 274 amino acids
Theoretical weight: 31.95 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P32496 (Residues: 1-274; Coverage: 100%)
Gene names: NIN1, RPN12, YFR052W
Sequence domains: CSN8/PSMD8/EIF3K family
26S proteasome complex subunit SEM1 Chain: I
Molecule details ›
Chain: I
Length: 89 amino acids
Theoretical weight: 10.4 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O94742 (Residues: 1-89; Coverage: 100%)
Gene names: DSH1, SEM1, YDR363W-A
Sequence domains: DSS1/SEM1 family

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.5Å
Relevant EMDB volumes: EMD-6479
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

25 review citations

Breaking the chains: deubiquitylating enzyme specificity begets function.
Clague et al. (2019)
24 more

7 mentions without citation

Proteasome Structure and Assembly.
Budenholzer et al. (2017)
6 more