› 5mpd

Electron Microscopy
4.1Å resolution

26S proteasome in presence of ATP (s1)

Released:
DOI: 10.2210/pdb5mpd/pdb
PDB entry 5mpd coloured by chain, front view.
PDB entry 5mpd coloured by chain, side view.
PDB entry 5mpd coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structural insights into the functional cycle of the ATPase module of the 26S proteasome.
Wehmer M, Rudack T, Beck F, Aufderheide A, Pfeifer G, Plitzko JM, Förster F, Schulten K, Baumeister W, Sakata E
Proc Natl Acad Sci U S A 114 1305-1310 (2017)
PMID: 28115689
Related structures: EMD-3534

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 tridecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126894 (preferred)
Entry contents:
13 distinct polypeptide molecules
Macromolecules (13 distinct):
26S proteasome regulatory subunit RPN10 Chain: W
Molecule details ›
Chain: W
Length: 268 amino acids
Theoretical weight: 29.78 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38886 (Residues: 1-268; Coverage: 100%)
Gene names: MCB1, RPN10, SUN1, YHR200W
Sequence domains: von Willebrand factor type A domain
Ubiquitin carboxyl-terminal hydrolase RPN11 Chain: V
Molecule details ›
Chain: V
Length: 306 amino acids
Theoretical weight: 34.44 KDa
Source organism: Saccharomyces cerevisiae S288C
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: T
Molecule details ›
Chain: T
Length: 274 amino acids
Theoretical weight: 31.95 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32496 (Residues: 1-274; Coverage: 100%)
Gene names: NIN1, RPN12, YFR052W
Sequence domains: CSN8/PSMD8/EIF3K family
26S proteasome regulatory subunit RPN13 Chain: X
Molecule details ›
Chain: X
Length: 156 amino acids
Theoretical weight: 17.92 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: O13563 (Residues: 1-156; Coverage: 100%)
Gene names: DAQ1, RPN13, YLR421C
Sequence domains: Proteasome complex subunit Rpn13, Pru domain
26S proteasome complex subunit SEM1 Chain: Y
Molecule details ›
Chain: Y
Length: 89 amino acids
Theoretical weight: 10.4 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: O94742 (Residues: 1-89; Coverage: 100%)
Gene names: DSH1, SEM1, YDR363W-A
Sequence domains: DSS1/SEM1 family
26S proteasome regulatory subunit RPN1 Chain: Z
Molecule details ›
Chain: Z
Length: 993 amino acids
Theoretical weight: 109.6 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38764 (Residues: 1-993; Coverage: 100%)
Gene names: HRD2, NAS1, RPD1, RPN1, YHR027C
Sequence domains:
26S proteasome regulatory subunit RPN2 Chain: N
Molecule details ›
Chain: N
Length: 945 amino acids
Theoretical weight: 104.35 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32565 (Residues: 1-945; Coverage: 100%)
Gene names: RPN2, SEN3, YIL075C
Sequence domains:
26S proteasome regulatory subunit RPN3 Chain: S
Molecule details ›
Chain: S
Length: 523 amino acids
Theoretical weight: 60.46 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40016 (Residues: 1-523; Coverage: 100%)
Gene names: RPN3, SUN2, YER021W
Sequence domains:
26S proteasome regulatory subunit RPN5 Chain: P
Molecule details ›
Chain: P
Length: 445 amino acids
Theoretical weight: 51.84 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12250 (Residues: 1-445; Coverage: 100%)
Gene names: D1572, NAS5, RPN5, YDL147W
Sequence domains:
26S proteasome regulatory subunit RPN6 Chain: Q
Molecule details ›
Chain: Q
Length: 434 amino acids
Theoretical weight: 49.84 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12377 (Residues: 1-434; Coverage: 100%)
Gene names: D2381, NAS4, RPN6, YDL097C
Sequence domains:
26S proteasome regulatory subunit RPN7 Chain: R
Molecule details ›
Chain: R
Length: 429 amino acids
Theoretical weight: 49.02 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06103 (Residues: 1-429; Coverage: 100%)
Gene names: P8283.8, RPN7, YPR108W
Sequence domains:
26S proteasome regulatory subunit RPN8 Chain: U
Molecule details ›
Chain: U
Length: 338 amino acids
Theoretical weight: 38.37 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q08723 (Residues: 1-338; Coverage: 100%)
Gene names: O5360, RPN8, YOR261C
Sequence domains:
26S proteasome regulatory subunit RPN9 Chain: O
Molecule details ›
Chain: O
Length: 393 amino acids
Theoretical weight: 45.84 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q04062 (Residues: 1-393; Coverage: 100%)
Gene names: D9461.14, NAS7, RPN9, YDR427W
Sequence domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.1Å
Relevant EMDB volumes: EMD-3534

Quick links

Citations

27 review citations

The Logic of the 26S Proteasome.
Collins et al. (2017)
26 more

9 mentions without citation

Structure and Function of the 26S Proteasome.
Bard et al. (2018)
8 more