› 6ef1

Electron Microscopy
4.73Å resolution

Yeast 26S proteasome bound to ubiquitinated substrate (5D motor state)

Released:
DOI: 10.2210/pdb6ef1/pdb
PDB entry 6ef1 coloured by chain, front view.
PDB entry 6ef1 coloured by chain, side view.
PDB entry 6ef1 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-9043

Function and Biology Details

Reaction catalysed: 
Cleavage of peptide bonds with very broad specificity.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetradecamer (preferred)
PDBe Complex ID:
PDB-CPX-139776 (preferred)
Entry contents:
14 distinct polypeptide molecules
Macromolecules (14 distinct):
Proteasome subunit alpha type-1 Chain: A
Molecule details ›
Chain: A
Length: 239 amino acids
Theoretical weight: 26.91 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P21243 (Residues: 13-251; Coverage: 95%)
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: 238 amino acids
Theoretical weight: 26.31 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P23638 (Residues: 8-245; Coverage: 92%)
Gene names: PRE9, PRS5, YGR135W
Sequence domains:
Proteasome subunit alpha type-4 Chain: D
Molecule details ›
Chain: D
Length: 234 amino acids
Theoretical weight: 26.1 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P40303 (Residues: 9-242; Coverage: 92%)
Gene names: PRE6, YOL038W
Sequence domains:
Proteasome subunit alpha type-5 Chain: E
Molecule details ›
Chain: E
Length: 242 amino acids
Theoretical weight: 26.54 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P32379 (Residues: 9-250; Coverage: 93%)
Gene names: DOA5, G9155, PUP2, YGR253C
Sequence domains:
Proteasome subunit alpha type-6 Chain: F
Molecule details ›
Chain: F
Length: 233 amino acids
Theoretical weight: 25.5 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P40302 (Residues: 2-234; Coverage: 100%)
Gene names: PRE5, YM9924.06, YMR314W
Sequence domains:
Probable proteasome subunit alpha type-7 Chain: G
Molecule details ›
Chain: G
Length: 243 amino acids
Theoretical weight: 26.84 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P21242 (Residues: 6-248; Coverage: 84%)
Gene names: O6650, PRC1, PRE10, PRS1, YOR362C
Sequence domains:
26S proteasome regulatory subunit 7 homolog Chain: H
Molecule details ›
Chain: H
Length: 262 amino acids
Theoretical weight: 29.07 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P33299 (Residues: 194-455; Coverage: 56%)
Gene names: CIM5, RPT1, YKL145W, YTA3
Sequence domains:
26S proteasome regulatory subunit 4 homolog Chain: I
Molecule details ›
Chain: I
Length: 271 amino acids
Theoretical weight: 30.13 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P40327 (Residues: 167-437; Coverage: 62%)
Gene names: D2920, RPT2, YDL007W, YHS4, YTA5
Sequence domains:
26S proteasome regulatory subunit 8 homolog Chain: J
Molecule details ›
Chain: J
Length: 273 amino acids
Theoretical weight: 30.24 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: Q01939 (Residues: 133-405; Coverage: 67%)
Gene names: CIM3, CRL3, RPT6, SUG1, TBPY, TBY1, YGL048C
Sequence domains:
26S proteasome regulatory subunit 6B homolog Chain: K
Molecule details ›
Chain: K
Length: 276 amino acids
Theoretical weight: 30.79 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P33298 (Residues: 153-428; Coverage: 65%)
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: 271 amino acids
Theoretical weight: 30.17 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P53549 (Residues: 166-436; Coverage: 62%)
Gene names: CRL13, PCS1, RPT4, SUG2, YOR259C
Sequence domains:
26S proteasome regulatory subunit 6A Chain: M
Molecule details ›
Chain: M
Length: 262 amino acids
Theoretical weight: 28.94 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae W303
UniProt:
  • Canonical: P33297 (Residues: 173-434; Coverage: 60%)
Gene names: O3258, RPT5, YOR117W, YOR3258W, YTA1
Sequence domains:
G2/mitotic-specific cyclin-B Chain: s
Molecule details ›
Chain: s
Length: 15 amino acids
Theoretical weight: 1.46 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P07818 (Residues: 22-36; Coverage: 4%)

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: 4.73Å
Relevant EMDB volumes: EMD-9043
Expression systems:
  • Saccharomyces cerevisiae W303
  • Escherichia coli BL21

Quick links

Citations

40 review citations

Dynamic Regulation of the 26S Proteasome: From Synthesis to Degradation.
Marshall et al. (2019)
39 more

4 mentions without citation

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