› 5wvk

Electron Microscopy
4.2Å resolution

Yeast proteasome-ADP-AlFx

Released:
DOI: 10.2210/pdb5wvk/pdb
PDB entry 5wvk coloured by chain, front view.
PDB entry 5wvk coloured by chain, side view.
PDB entry 5wvk coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
High-resolution cryo-EM structure of the proteasome in complex with ADP-AlFx.
Ding Z, Fu Z, Xu C, Wang Y, Wang Y, Li J, Kong L, Chen J, Li N, Zhang R, Cong Y
Cell Res 27 373-385 (2017)
PMID: 28106073
Related structures: EMD-6694

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 beta type-1 Chains: 1, b
Molecule details ›
Chains: 1, b
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, h
Molecule details ›
Chains: 3, h
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, g
Molecule details ›
Chains: 4, g
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, f
Molecule details ›
Chains: 5, f
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, e
Molecule details ›
Chains: 6, e
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, a
Molecule details ›
Chains: 7, a
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
Proteasome subunit alpha type-1 Chains: A, c
Molecule details ›
Chains: A, c
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, j
Molecule details ›
Chains: B, j
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, d
Molecule details ›
Chains: C, d
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, n
Molecule details ›
Chains: D, n
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, m
Molecule details ›
Chains: E, m
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, l
Molecule details ›
Chains: F, l
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, k
Molecule details ›
Chains: G, k
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:
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 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 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 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 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:
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 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 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 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:
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 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
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:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.2Å
Relevant EMDB volumes: EMD-6694

Quick links

Citations

13 review citations

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

4 mentions without citation

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