6fvw

Electron Microscopy
4.5Å resolution

26S proteasome, s4 state

Released:

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:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 47-mer (preferred)
Entry contents:
33 distinct polypeptide molecules
Macromolecules (33 distinct):
Proteasome subunit alpha type-1 Chains: A, a
Molecule details ›
Chains: A, a
Length: 244 amino acids
Theoretical weight: 27.36 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P21243 (Residues: 8-251; Coverage: 97%)
Gene names: PRC2, PRS2, SCL1, YGL011C
Sequence domains: Proteasome subunit A N-terminal signature
Proteasome subunit alpha type-2 Chains: B, b
Molecule details ›
Chains: B, b
Length: 247 amino acids
Theoretical weight: 26.84 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P23639 (Residues: 4-250; Coverage: 99%)
Gene names: PRE8, PRS4, YML092C
Sequence domains: Proteasome subunit A N-terminal signature
Proteasome subunit alpha type-3 Chains: C, c
Molecule details ›
Chains: C, c
Length: 241 amino acids
Theoretical weight: 26.75 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P23638 (Residues: 5-245; Coverage: 93%)
Gene names: PRE9, PRS5, YGR135W
Sequence domains: Proteasome subunit A N-terminal signature
Proteasome subunit alpha type-4 Chains: D, d
Molecule details ›
Chains: D, d
Length: 252 amino acids
Theoretical weight: 28.26 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40303 (Residues: 3-254; Coverage: 99%)
Gene names: PRE6, YOL038W
Sequence domains: Proteasome subunit A N-terminal signature
Proteasome subunit alpha type-5 Chains: E, e
Molecule details ›
Chains: E, e
Length: 245 amino acids
Theoretical weight: 26.92 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32379 (Residues: 6-250; Coverage: 94%)
Gene names: DOA5, G9155, PUP2, YGR253C
Sequence domains: Proteasome subunit A N-terminal signature
Proteasome subunit alpha type-6 Chains: F, f
Molecule details ›
Chains: F, f
Length: 232 amino acids
Theoretical weight: 25.36 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40302 (Residues: 3-234; Coverage: 99%)
Gene names: PRE5, YM9924.06, YMR314W
Sequence domains: Proteasome subunit A N-terminal signature
Probable proteasome subunit alpha type-7 Chains: G, g
Molecule details ›
Chains: G, g
Length: 245 amino acids
Theoretical weight: 27.01 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P21242 (Residues: 4-248; Coverage: 85%)
Gene names: O6650, PRC1, PRE10, PRS1, YOR362C
Sequence domains: Proteasome subunit A N-terminal signature
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
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
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
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
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
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
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
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
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: Proteasome/cyclosome repeat
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: PCI domain
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: PCI domain
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: PCI domain
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: JAB1/Mov34/MPN/PAD-1 ubiquitin protease
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: 426 amino acids
Theoretical weight: 47.32 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P33299 (Residues: 42-467; Coverage: 91%)
Gene names: CIM5, RPT1, YKL145W, YTA3
Sequence domains: ATPase family associated with various cellular activities (AAA)
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: ATPase family associated with various cellular activities (AAA)
26S proteasome regulatory subunit 6B homolog Chain: K
Molecule details ›
Chain: K
Length: 384 amino acids
Theoretical weight: 43.33 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P33298 (Residues: 45-428; Coverage: 90%)
Gene names: D9509.14, RPT3, YDR394W, YNT1, YTA2
Sequence domains: ATPase family associated with various cellular activities (AAA)
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: ATPase family associated with various cellular activities (AAA)
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: 403 amino acids
Theoretical weight: 45.11 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q01939 (Residues: 3-405; Coverage: 100%)
Gene names: CIM3, CRL3, RPT6, SUG1, TBPY, TBY1, YGL048C
Sequence domains: ATPase family associated with various cellular activities (AAA)

Ligands and Environments

3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.5Å
Relevant EMDB volumes: EMD-4322