› 6ef3

Electron Microscopy
4.17Å resolution

Yeast 26S proteasome bound to ubiquitinated substrate (4D motor state)

Released:
DOI: 10.2210/pdb6ef3/pdb
PDB entry 6ef3 coloured by chain, front view.
PDB entry 6ef3 coloured by chain, side view.
PDB entry 6ef3 coloured by chain, top view.
Source organisms:
Primary publication:
Substrate-engaged 26S proteasome structures reveal mechanisms for ATP-hydrolysis-driven translocation.
de la Peña AH, Goodall EA, Gates SN, Lander GC, Martin A
Science 362 (2018)
PMID: 30309908
Related structures: EMD-9045

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 24-mer (preferred)
PDBe Complex ID:
PDB-CPX-139775 (preferred)
Entry contents:
24 distinct polypeptide molecules
Macromolecules (24 distinct):
Proteasome subunit beta type-1 Chain: 1
Molecule details ›
Chain: 1
Length: 215 amino acids
Theoretical weight: 23.57 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P38624 (Residues: 1-215; Coverage: 100%)
Gene names: J1407, PRE3, YJL001W
Sequence domains: Proteasome subunit
Proteasome subunit beta type-2 Chain: 2
Molecule details ›
Chain: 2
Length: 261 amino acids
Theoretical weight: 28.3 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P25043 (Residues: 1-261; Coverage: 100%)
Gene names: PUP1, YOR157C
Sequence domains:
Proteasome subunit beta type-3 Chain: 3
Molecule details ›
Chain: 3
Length: 205 amino acids
Theoretical weight: 22.63 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P25451 (Residues: 1-205; Coverage: 100%)
Gene names: PUP3, YER094C
Sequence domains: Proteasome subunit
Proteasome subunit beta type-4 Chain: 4
Molecule details ›
Chain: 4
Length: 198 amino acids
Theoretical weight: 22.55 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P22141 (Residues: 1-198; Coverage: 100%)
Gene names: PRE1, YER012W
Sequence domains: Proteasome subunit
Proteasome subunit beta type-5 Chain: 5
Molecule details ›
Chain: 5
Length: 287 amino acids
Theoretical weight: 31.67 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
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 Chain: 6
Molecule details ›
Chain: 6
Length: 241 amino acids
Theoretical weight: 26.91 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P23724 (Residues: 1-241; Coverage: 100%)
Gene names: PRE7, PRS3, PTS1, YBL0407, YBL041W
Sequence domains: Proteasome subunit
Proteasome subunit beta type-7 Chain: 7
Molecule details ›
Chain: 7
Length: 266 amino acids
Theoretical weight: 29.47 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P30657 (Residues: 1-266; Coverage: 100%)
Gene names: PRE4, YFR050C
Sequence domains: Proteasome subunit
Proteasome subunit alpha type-1 Chain: A
Molecule details ›
Chain: A
Length: 252 amino acids
Theoretical weight: 28.03 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P21243 (Residues: 1-252; Coverage: 100%)
Gene names: PRC2, PRS2, SCL1, YGL011C
Sequence domains:
Proteasome subunit alpha type-2 Chain: B
Molecule details ›
Chain: B
Length: 250 amino acids
Theoretical weight: 27.19 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P23639 (Residues: 1-250; Coverage: 100%)
Gene names: PRE8, PRS4, YML092C
Sequence domains:
Proteasome subunit alpha type-3 Chain: C
Molecule details ›
Chain: C
Length: 258 amino acids
Theoretical weight: 28.75 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P23638 (Residues: 1-258; Coverage: 100%)
Gene names: PRE9, PRS5, YGR135W
Sequence domains:
Proteasome subunit alpha type-4 Chain: D
Molecule details ›
Chain: D
Length: 254 amino acids
Theoretical weight: 28.48 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P40303 (Residues: 1-254; Coverage: 100%)
Gene names: PRE6, YOL038W
Sequence domains:
Proteasome subunit alpha type-5 Chain: E
Molecule details ›
Chain: E
Length: 260 amino acids
Theoretical weight: 28.65 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P32379 (Residues: 1-260; Coverage: 100%)
Gene names: DOA5, G9155, PUP2, YGR253C
Sequence domains:
Proteasome subunit alpha type-6 Chain: F
Molecule details ›
Chain: F
Length: 234 amino acids
Theoretical weight: 25.63 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P40302 (Residues: 1-234; Coverage: 100%)
Gene names: PRE5, YM9924.06, YMR314W
Sequence domains:
Probable proteasome subunit alpha type-7 Chain: G
Molecule details ›
Chain: G
Length: 288 amino acids
Theoretical weight: 31.58 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
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
Expression system: Saccharomyces cerevisiae W303
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
Expression system: Saccharomyces cerevisiae W303
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
Expression system: Saccharomyces cerevisiae W303
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
Expression system: Saccharomyces cerevisiae W303
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
Expression system: Saccharomyces cerevisiae W303
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
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P33297 (Residues: 1-434; Coverage: 100%)
Gene names: O3258, RPT5, YOR117W, YOR3258W, YTA1
Sequence domains:
Proteasome subunit beta type-7 Chain: n
Molecule details ›
Chain: n
Length: 15 amino acids
Theoretical weight: 1.79 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P30657 (Residues: 251-265; Coverage: 6%)
Gene names: PRE4, YFR050C
Ubiquitin carboxyl-terminal hydrolase RPN11 Chain: r
Molecule details ›
Chain: r
Length: 306 amino acids
Theoretical weight: 34.44 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P43588 (Residues: 1-306; Coverage: 100%)
Gene names: MPR1, RPN11, YFR004W
Sequence domains: JAB1/Mov34/MPN/PAD-1 ubiquitin protease
G2/mitotic-specific cyclin-B Chain: s
Molecule details ›
Chain: s
Length: 38 amino acids
Theoretical weight: 4.07 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P07818 (Residues: 16-41; Coverage: 6%)
Ubiquitin-ribosomal protein eL40A fusion protein Chain: u
Molecule details ›
Chain: u
Length: 128 amino acids
Theoretical weight: 14.58 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli B
UniProt:
  • Canonical: P0CH08 (Residues: 1-128; Coverage: 100%)
Gene names: RPL40A, UBI1, YIL148W
Sequence domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 4.17Å
Relevant EMDB volumes: EMD-9045
Expression systems:
  • Saccharomyces cerevisiae W303
  • Escherichia coli BL21
  • Escherichia coli B

Quick links

Citations

38 review citations

The molecular principles governing the activity and functional diversity of AAA+ proteins.
Puchades et al. (2020)
37 more

13 mentions without citation

Stairway to translocation: AAA+ motor structures reveal the mechanisms of ATP-dependent substrate translocation.
Gates et al. (2020)
12 more