› 5mpc

Electron Microscopy
7.7Å resolution

26S proteasome in presence of BeFx (s4)

Released:
DOI: 10.2210/pdb5mpc/pdb
PDB entry 5mpc coloured by chain, front view.
PDB entry 5mpc coloured by chain, side view.
PDB entry 5mpc 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-3537

Function and Biology Details

Reactions catalysed: 
Cleavage of peptide bonds with very broad specificity.
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 48-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-517931 (preferred)
Entry contents:
34 distinct polypeptide molecules
Macromolecules (34 distinct):
Proteasome subunit alpha type-1 Chains: A, a
Molecule details ›
Chains: A, a
Length: 252 amino acids
Theoretical weight: 28.03 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P21243 (Residues: 1-252; Coverage: 100%)
Gene names: PRC2, PRS2, SCL1, YGL011C
Sequence domains:
Proteasome subunit alpha type-2 Chains: B, b
Molecule details ›
Chains: B, b
Length: 250 amino acids
Theoretical weight: 27.19 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P23639 (Residues: 1-250; Coverage: 100%)
Gene names: PRE8, PRS4, YML092C
Sequence domains:
Proteasome subunit alpha type-3 Chains: C, c
Molecule details ›
Chains: C, c
Length: 258 amino acids
Theoretical weight: 28.75 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P23638 (Residues: 1-258; Coverage: 100%)
Gene names: PRE9, PRS5, YGR135W
Sequence domains:
Proteasome subunit alpha type-4 Chains: D, d
Molecule details ›
Chains: D, d
Length: 254 amino acids
Theoretical weight: 28.48 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40303 (Residues: 1-254; Coverage: 100%)
Gene names: PRE6, YOL038W
Sequence domains:
Proteasome subunit alpha type-5 Chains: E, e
Molecule details ›
Chains: E, e
Length: 260 amino acids
Theoretical weight: 28.65 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32379 (Residues: 1-260; Coverage: 100%)
Gene names: DOA5, G9155, PUP2, YGR253C
Sequence domains:
Proteasome subunit alpha type-6 Chains: F, f
Molecule details ›
Chains: F, f
Length: 234 amino acids
Theoretical weight: 25.63 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40302 (Residues: 1-234; Coverage: 100%)
Gene names: PRE5, YM9924.06, YMR314W
Sequence domains:
Probable proteasome subunit alpha type-7 Chains: G, g
Molecule details ›
Chains: G, g
Length: 288 amino acids
Theoretical weight: 31.58 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P21242 (Residues: 1-288; Coverage: 100%)
Gene names: O6650, PRC1, PRE10, PRS1, YOR362C
Sequence domains:
Proteasome subunit beta type-1 Chains: 1, h
Molecule details ›
Chains: 1, h
Length: 215 amino acids
Theoretical weight: 23.57 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38624 (Residues: 1-215; Coverage: 100%)
Gene names: J1407, PRE3, YJL001W
Sequence domains: Proteasome subunit
Proteasome subunit beta type-2 Chains: 2, i
Molecule details ›
Chains: 2, i
Length: 261 amino acids
Theoretical weight: 28.3 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25043 (Residues: 1-261; Coverage: 100%)
Gene names: PUP1, YOR157C
Sequence domains:
Proteasome subunit beta type-3 Chains: 3, j
Molecule details ›
Chains: 3, j
Length: 205 amino acids
Theoretical weight: 22.63 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25451 (Residues: 1-205; Coverage: 100%)
Gene names: PUP3, YER094C
Sequence domains: Proteasome subunit
Proteasome subunit beta type-4 Chains: 4, k
Molecule details ›
Chains: 4, k
Length: 198 amino acids
Theoretical weight: 22.55 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P22141 (Residues: 1-198; Coverage: 100%)
Gene names: PRE1, YER012W
Sequence domains: Proteasome subunit
Proteasome subunit beta type-5 Chains: 5, l
Molecule details ›
Chains: 5, l
Length: 287 amino acids
Theoretical weight: 31.67 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P30656 (Residues: 1-287; Coverage: 100%)
Gene names: DOA3, P8283.10, PRE2, PRG1, YPR103W
Sequence domains: Proteasome subunit
Proteasome subunit beta type-6 Chains: 6, m
Molecule details ›
Chains: 6, m
Length: 241 amino acids
Theoretical weight: 26.91 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P23724 (Residues: 1-241; Coverage: 100%)
Gene names: PRE7, PRS3, PTS1, YBL0407, YBL041W
Sequence domains: Proteasome subunit
Proteasome subunit beta type-7 Chains: 7, n
Molecule details ›
Chains: 7, n
Length: 266 amino acids
Theoretical weight: 29.47 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P30657 (Residues: 1-266; Coverage: 100%)
Gene names: PRE4, YFR050C
Sequence domains: Proteasome subunit
26S proteasome regulatory subunit 7 homolog Chain: H
Molecule details ›
Chain: H
Length: 467 amino acids
Theoretical weight: 52.05 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P33299 (Residues: 1-467; Coverage: 100%)
Gene names: CIM5, RPT1, YKL145W, YTA3
Sequence domains:
26S proteasome regulatory subunit 4 homolog Chain: I
Molecule details ›
Chain: I
Length: 437 amino acids
Theoretical weight: 48.9 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40327 (Residues: 1-437; Coverage: 100%)
Gene names: D2920, RPT2, YDL007W, YHS4, YTA5
Sequence domains:
26S proteasome regulatory subunit 6B homolog Chain: K
Molecule details ›
Chain: K
Length: 428 amino acids
Theoretical weight: 47.95 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P33298 (Residues: 1-428; Coverage: 100%)
Gene names: D9509.14, RPT3, YDR394W, YNT1, YTA2
Sequence domains:
26S proteasome subunit RPT4 Chain: L
Molecule details ›
Chain: L
Length: 437 amino acids
Theoretical weight: 49.48 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53549 (Residues: 1-437; Coverage: 100%)
Gene names: CRL13, PCS1, RPT4, SUG2, YOR259C
Sequence domains:
26S proteasome regulatory subunit 6A Chain: M
Molecule details ›
Chain: M
Length: 434 amino acids
Theoretical weight: 48.32 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P33297 (Residues: 1-434; Coverage: 100%)
Gene names: O3258, RPT5, YOR117W, YOR3258W, YTA1
Sequence domains:
26S proteasome regulatory subunit 8 homolog Chain: J
Molecule details ›
Chain: J
Length: 405 amino acids
Theoretical weight: 45.34 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q01939 (Residues: 1-405; Coverage: 100%)
Gene names: CIM3, CRL3, RPT6, SUG1, TBPY, TBY1, YGL048C
Sequence domains:
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:
Ubiquitin carboxyl-terminal hydrolase 6 Chain: 8
Molecule details ›
Chain: 8
Length: 499 amino acids
Theoretical weight: 57.19 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P43593 (Residues: 1-499; Coverage: 100%)
Gene names: UBP6, YFR010W
Sequence domains: Ubiquitin carboxyl-terminal hydrolase

Ligands and Environments

3 bound ligands:
Ligand ATP 4 x ATP
Ligand MG 6 x MG
Ligand ADP 2 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 7.7Å
Relevant EMDB volumes: EMD-3537

Quick links

Citations

30 review citations

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

7 mentions without citation

Functional Differences between Proteasome Subtypes.
Abi Habib et al. (2022)
6 more