5mpd

Electron Microscopy
4.1Å resolution

26S proteasome in presence of ATP (s1)

Released:

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:
Cellular component:

Structure analysis Details

Assembly composition:
hetero tridecamer (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:
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 ubiquitin receptor
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