› 6fvv

Electron Microscopy
5.4Å resolution

26S proteasome, s3 state

Released:
DOI: 10.2210/pdb6fvv/pdb
PDB entry 6fvv coloured by chain, front view.
PDB entry 6fvv coloured by chain, side view.
PDB entry 6fvv coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Expanded Coverage of the 26S Proteasome Conformational Landscape Reveals Mechanisms of Peptidase Gating.
Eisele MR, Reed RG, Rudack T, Schweitzer A, Beck F, Nagy I, Pfeifer G, Plitzko JM, Baumeister W, Tomko RJ, Sakata E
Cell Rep 24 1301-1315.e5 (2018)
PMID: 30067984
Related structures: EMD-4321

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 47-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126892 (preferred)
Entry contents:
33 distinct polypeptide molecules
Macromolecules (33 distinct):
Proteasome subunit alpha type-1 Chains: A, a
Molecule details ›
Chains: A, a
Length: 241 amino acids
Theoretical weight: 27.13 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P21243 (Residues: 11-251; Coverage: 96%)
Gene names: PRC2, PRS2, SCL1, YGL011C
Sequence domains:
Proteasome subunit alpha type-2 Chains: B, b
Molecule details ›
Chains: B, b
Length: 249 amino acids
Theoretical weight: 27.06 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P23639 (Residues: 2-250; Coverage: 100%)
Gene names: PRE8, PRS4, YML092C
Sequence domains:
Proteasome subunit alpha type-3 Chains: C, c
Molecule details ›
Chains: C, c
Length: 244 amino acids
Theoretical weight: 27.05 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P23638 (Residues: 2-245; Coverage: 95%)
Gene names: PRE9, PRS5, YGR135W
Sequence domains:
Proteasome subunit alpha type-4 Chains: D, d
Molecule details ›
Chains: D, d
Length: 251 amino acids
Theoretical weight: 28.2 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40303 (Residues: 4-254; Coverage: 99%)
Gene names: PRE6, YOL038W
Sequence domains:
Proteasome subunit alpha type-5 Chains: E, e
Molecule details ›
Chains: E, e
Length: 244 amino acids
Theoretical weight: 26.84 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32379 (Residues: 7-250; Coverage: 94%)
Gene names: DOA5, G9155, PUP2, YGR253C
Sequence domains:
Proteasome subunit alpha type-6 Chains: F, f
Molecule details ›
Chains: F, f
Length: 231 amino acids
Theoretical weight: 25.2 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40302 (Residues: 4-234; Coverage: 99%)
Gene names: PRE5, YM9924.06, YMR314W
Sequence domains:
Probable proteasome subunit alpha type-7 Chains: G, g
Molecule details ›
Chains: G, g
Length: 242 amino acids
Theoretical weight: 26.73 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P21242 (Residues: 7-248; Coverage: 84%)
Gene names: O6650, PRC1, PRE10, PRS1, YOR362C
Sequence domains:
Proteasome subunit beta type-1 Chains: 1, h
Molecule details ›
Chains: 1, h
Length: 196 amino acids
Theoretical weight: 21.52 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38624 (Residues: 20-215; Coverage: 91%)
Gene names: J1407, PRE3, YJL001W
Sequence domains: Proteasome subunit
Proteasome subunit beta type-2 Chains: 2, i
Molecule details ›
Chains: 2, i
Length: 226 amino acids
Theoretical weight: 24.49 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25043 (Residues: 30-255; Coverage: 87%)
Gene names: PUP1, YOR157C
Sequence domains:
Proteasome subunit beta type-3 Chains: 3, j
Molecule details ›
Chains: 3, j
Length: 204 amino acids
Theoretical weight: 22.5 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25451 (Residues: 2-205; Coverage: 100%)
Gene names: PUP3, YER094C
Sequence domains: Proteasome subunit
Proteasome subunit beta type-4 Chains: 4, k
Molecule details ›
Chains: 4, k
Length: 195 amino acids
Theoretical weight: 22.22 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P22141 (Residues: 1-195; Coverage: 99%)
Gene names: PRE1, YER012W
Sequence domains: Proteasome subunit
Proteasome subunit beta type-5 Chains: 5, l
Molecule details ›
Chains: 5, l
Length: 212 amino acids
Theoretical weight: 23.33 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P30656 (Residues: 76-287; Coverage: 74%)
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: 222 amino acids
Theoretical weight: 24.88 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P23724 (Residues: 20-241; Coverage: 92%)
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: 232 amino acids
Theoretical weight: 25.83 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P30657 (Residues: 34-265; Coverage: 87%)
Gene names: PRE4, YFR050C
Sequence domains: Proteasome subunit
26S proteasome regulatory subunit RPN10 Chain: W
Molecule details ›
Chain: W
Length: 197 amino acids
Theoretical weight: 21.82 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38886 (Residues: 1-197; Coverage: 74%)
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: 289 amino acids
Theoretical weight: 32.49 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P43588 (Residues: 18-306; Coverage: 94%)
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: 266 amino acids
Theoretical weight: 31.11 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32496 (Residues: 7-272; Coverage: 97%)
Gene names: NIN1, RPN12, YFR052W
Sequence domains: CSN8/PSMD8/EIF3K family
26S proteasome regulatory subunit RPN13 Chain: X
Molecule details ›
Chain: X
Length: 127 amino acids
Theoretical weight: 14.65 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: O13563 (Residues: 7-133; Coverage: 81%)
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: 970 amino acids
Theoretical weight: 106.9 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38764 (Residues: 1-970; Coverage: 98%)
Gene names: HRD2, NAS1, RPD1, RPN1, YHR027C
Sequence domains:
26S proteasome regulatory subunit RPN2 Chain: N
Molecule details ›
Chain: N
Length: 922 amino acids
Theoretical weight: 101.89 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32565 (Residues: 4-925; Coverage: 98%)
Gene names: RPN2, SEN3, YIL075C
Sequence domains:
26S proteasome regulatory subunit RPN3 Chain: S
Molecule details ›
Chain: S
Length: 475 amino acids
Theoretical weight: 55.38 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40016 (Residues: 18-492; Coverage: 91%)
Gene names: RPN3, SUN2, YER021W
Sequence domains:
26S proteasome regulatory subunit RPN5 Chain: P
Molecule details ›
Chain: P
Length: 440 amino acids
Theoretical weight: 51.34 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12250 (Residues: 1-440; Coverage: 99%)
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: 405 amino acids
Theoretical weight: 46.31 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06103 (Residues: 20-424; Coverage: 94%)
Gene names: P8283.8, RPN7, YPR108W
Sequence domains:
26S proteasome regulatory subunit RPN8 Chain: U
Molecule details ›
Chain: U
Length: 304 amino acids
Theoretical weight: 34.56 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q08723 (Residues: 1-304; Coverage: 90%)
Gene names: O5360, RPN8, YOR261C
Sequence domains:
26S proteasome regulatory subunit RPN9 Chain: O
Molecule details ›
Chain: O
Length: 388 amino acids
Theoretical weight: 45.19 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q04062 (Residues: 6-393; Coverage: 99%)
Gene names: D9461.14, NAS7, RPN9, YDR427W
Sequence domains:
26S proteasome regulatory subunit 7 homolog Chain: H
Molecule details ›
Chain: H
Length: 417 amino acids
Theoretical weight: 46.19 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P33299 (Residues: 42-458; Coverage: 89%)
Gene names: CIM5, RPT1, YKL145W, YTA3
Sequence domains:
26S proteasome regulatory subunit 4 homolog Chain: I
Molecule details ›
Chain: I
Length: 385 amino acids
Theoretical weight: 43.23 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40327 (Residues: 53-437; Coverage: 88%)
Gene names: D2920, RPT2, YDL007W, YHS4, YTA5
Sequence domains:
26S proteasome regulatory subunit 6B homolog Chain: K
Molecule details ›
Chain: K
Length: 394 amino acids
Theoretical weight: 44.35 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P33298 (Residues: 35-428; Coverage: 92%)
Gene names: D9509.14, RPT3, YDR394W, YNT1, YTA2
Sequence domains:
26S proteasome subunit RPT4 Chain: L
Molecule details ›
Chain: L
Length: 388 amino acids
Theoretical weight: 43.93 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53549 (Residues: 49-436; Coverage: 89%)
Gene names: CRL13, PCS1, RPT4, SUG2, YOR259C
Sequence domains:
26S proteasome regulatory subunit 6A Chain: M
Molecule details ›
Chain: M
Length: 421 amino acids
Theoretical weight: 46.9 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P33297 (Residues: 14-434; Coverage: 97%)
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:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 5.4Å
Relevant EMDB volumes: EMD-4321

Quick links

Citations

17 review citations

Mechanisms of substrate recognition by the 26S proteasome.
Davis et al. (2021)
16 more

3 mentions without citation

Expanded Coverage of the 26S Proteasome Conformational Landscape Reveals Mechanisms of Peptidase Gating.
Eisele et al. (2018)
2 more