› 6epd

Electron Microscopy
15.4Å resolution

Substrate processing state 26S proteasome (SPS1)

Released:
DOI: 10.2210/pdb6epd/pdb
PDB entry 6epd coloured by chain, front view.
PDB entry 6epd coloured by chain, side view.
PDB entry 6epd coloured by chain, top view.
Source organism: Rattus norvegicus
Primary publication:
In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment.
Guo Q, Lehmer C, Martínez-Sánchez A, Rudack T, Beck F, Hartmann H, Pérez-Berlanga M, Frottin F, Hipp MS, Hartl FU, Edbauer D, Baumeister W, Fernández-Busnadiego R
Cell 172 696-705.e12 (2018)
PMID: 29398115
Related structures: EMD-3914

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 32-mer (preferred)
PDBe Complex ID:
PDB-CPX-500788 (preferred)
Entry contents:
32 distinct polypeptide molecules
Macromolecules (32 distinct):
Proteasome subunit alpha type-6 Chain: A
Molecule details ›
Chain: A
Length: 246 amino acids
Theoretical weight: 27.43 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: P60901 (Residues: 1-246; Coverage: 100%)
Gene name: Psma6
Sequence domains:
Proteasome subunit alpha type-2 Chain: B
Molecule details ›
Chain: B
Length: 234 amino acids
Theoretical weight: 25.96 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: P17220 (Residues: 1-234; Coverage: 100%)
Gene name: Psma2
Sequence domains:
Proteasome subunit alpha type-4 Chain: C
Molecule details ›
Chain: C
Length: 261 amino acids
Theoretical weight: 29.54 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: P21670 (Residues: 1-261; Coverage: 100%)
Gene name: Psma4
Sequence domains:
Proteasome subunit alpha type-7 Chain: D
Molecule details ›
Chain: D
Length: 254 amino acids
Theoretical weight: 28.37 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: P48004 (Residues: 1-254; Coverage: 100%)
Gene name: Psma7
Sequence domains:
Proteasome subunit alpha type-5 Chain: E
Molecule details ›
Chain: E
Length: 241 amino acids
Theoretical weight: 26.42 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: P34064 (Residues: 1-241; Coverage: 100%)
Gene name: Psma5
Sequence domains:
Proteasome subunit alpha type-1 Chain: F
Molecule details ›
Chain: F
Length: 263 amino acids
Theoretical weight: 29.56 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: P18420 (Residues: 1-263; Coverage: 100%)
Gene name: Psma1
Sequence domains:
Proteasome subunit alpha type-3 Chain: G
Molecule details ›
Chain: G
Length: 255 amino acids
Theoretical weight: 28.46 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: P18422 (Residues: 1-255; Coverage: 100%)
Gene name: Psma3
Sequence domains:
Proteasome subunit beta type-6 Chain: 1
Molecule details ›
Chain: 1
Length: 238 amino acids
Theoretical weight: 25.31 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: P28073 (Residues: 1-238; Coverage: 100%)
Gene names: Psmb6, Psmb6l
Sequence domains: Proteasome subunit
Proteasome subunit beta type-7 Chain: 2
Molecule details ›
Chain: 2
Length: 277 amino acids
Theoretical weight: 29.96 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: Q9JHW0 (Residues: 1-277; Coverage: 100%)
Gene name: Psmb7
Sequence domains:
Proteasome subunit beta type-3 Chain: 3
Molecule details ›
Chain: 3
Length: 205 amino acids
Theoretical weight: 22.99 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: P40112 (Residues: 1-205; Coverage: 100%)
Gene name: Psmb3
Sequence domains: Proteasome subunit
Proteasome subunit beta type-2 Chain: 4
Molecule details ›
Chain: 4
Length: 201 amino acids
Theoretical weight: 22.94 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: P40307 (Residues: 1-201; Coverage: 100%)
Gene name: Psmb2
Sequence domains: Proteasome subunit
Proteasome subunit beta type-5 Chain: 5
Molecule details ›
Chain: 5
Length: 263 amino acids
Theoretical weight: 28.62 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: P28075 (Residues: 1-263; Coverage: 100%)
Gene name: Psmb5
Sequence domains: Proteasome subunit
Proteasome subunit beta type-1 Chain: 6
Molecule details ›
Chain: 6
Length: 240 amino acids
Theoretical weight: 26.51 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: P18421 (Residues: 1-240; Coverage: 100%)
Gene name: Psmb1
Sequence domains: Proteasome subunit
Proteasome subunit beta type-4 Chain: 7
Molecule details ›
Chain: 7
Length: 263 amino acids
Theoretical weight: 29.23 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: P34067 (Residues: 1-263; Coverage: 100%)
Gene name: Psmb4
Sequence domains: Proteasome subunit
26S proteasome non-ATPase regulatory subunit 4 Chain: W
Molecule details ›
Chain: W
Length: 377 amino acids
Theoretical weight: 40.78 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: Q9ESH1 (Residues: 1-377; Coverage: 100%)
Gene name: Psmd4
Sequence domains:
MPN domain-containing protein Chain: V
Molecule details ›
Chain: V
Length: 310 amino acids
Theoretical weight: 34.62 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: Q4V8E2 (Residues: 1-310; Coverage: 100%)
Gene name: Psmd14
Sequence domains: JAB1/Mov34/MPN/PAD-1 ubiquitin protease
26S proteasome non-ATPase regulatory subunit 8 Chain: T
Molecule details ›
Chain: T
Length: 353 amino acids
Theoretical weight: 39.93 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: F1LMQ3 (Residues: 1-353; Coverage: 100%)
Gene name: Psmd8
Sequence domains: CSN8/PSMD8/EIF3K family
26S proteasome complex subunit SEM1 Chain: Y
Molecule details ›
Chain: Y
Length: 70 amino acids
Theoretical weight: 8.28 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: D3ZHW9 (Residues: 1-70; Coverage: 100%)
Gene names: Sem1, Shfm1
Sequence domains: DSS1/SEM1 family
26S proteasome non-ATPase regulatory subunit 2 Chain: Z
Molecule details ›
Chain: Z
Length: 908 amino acids
Theoretical weight: 100.3 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: Q4FZT9 (Residues: 1-908; Coverage: 100%)
Gene name: Psmd2
Sequence domains:
26S proteasome non-ATPase regulatory subunit 1 Chain: N
Molecule details ›
Chain: N
Length: 953 amino acids
Theoretical weight: 105.87 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: O88761 (Residues: 1-953; Coverage: 100%)
Gene name: Psmd1
Sequence domains:
PCI domain-containing protein Chain: S
Molecule details ›
Chain: S
Length: 530 amino acids
Theoretical weight: 60.78 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: A6HIT6 (Residues: 1-530; Coverage: 100%)
Gene name: Psmd3
Sequence domains:
PCI domain-containing protein Chain: P
Molecule details ›
Chain: P
Length: 456 amino acids
Theoretical weight: 53.01 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: Q5XIC6 (Residues: 1-456; Coverage: 100%)
Gene name: Psmd12
Sequence domains:
26S proteasome non-ATPase regulatory subunit 11 Chain: Q
Molecule details ›
Chain: Q
Length: 422 amino acids
Theoretical weight: 47.53 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: F1LMZ8 (Residues: 1-422; Coverage: 100%)
Gene name: Psmd11
Sequence domains:
26S proteasome non-ATPase regulatory subunit 6 Chain: R
Molecule details ›
Chain: R
Length: 389 amino acids
Theoretical weight: 45.66 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: Q6PCT9 (Residues: 1-389; Coverage: 100%)
Gene names: Psmd6, rCG_42172
Sequence domains:
MPN domain-containing protein Chain: U
Molecule details ›
Chain: U
Length: 320 amino acids
Theoretical weight: 36.55 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: D4AEH3 (Residues: 1-82, 83-314; Coverage: 100%)
Gene name: Psmd7
Sequence domains:
26S proteasome non-ATPase regulatory subunit 13 Chain: O
Molecule details ›
Chain: O
Length: 376 amino acids
Theoretical weight: 42.87 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: B0BN93 (Residues: 1-376; Coverage: 100%)
Gene name: Psmd13
Sequence domains:
26S proteasome regulatory subunit 7 Chain: H
Molecule details ›
Chain: H
Length: 433 amino acids
Theoretical weight: 48.64 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: Q63347 (Residues: 1-433; Coverage: 100%)
Gene names: Mss1, Psmc2
Sequence domains:
26S proteasome regulatory subunit 4 Chain: I
Molecule details ›
Chain: I
Length: 440 amino acids
Theoretical weight: 49.26 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: P62193 (Residues: 1-440; Coverage: 100%)
Gene name: Psmc1
Sequence domains:
26S proteasome regulatory subunit 6B Chain: K
Molecule details ›
Chain: K
Length: 418 amino acids
Theoretical weight: 47.47 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: Q63570 (Residues: 1-418; Coverage: 100%)
Gene names: Psmc4, Tbp7
Sequence domains:
Proteasome 26S subunit, ATPase 6 Chain: L
Molecule details ›
Chain: L
Length: 403 amino acids
Theoretical weight: 45.87 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: G3V6W6 (Residues: 1-403; Coverage: 100%)
Gene names: LOC100365869, Psmc6
Sequence domains:
26S proteasome regulatory subunit 6A Chain: M
Molecule details ›
Chain: M
Length: 442 amino acids
Theoretical weight: 49.61 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: Q63569 (Residues: 1-439; Coverage: 100%)
Gene names: Psmc3, Tbp1
Sequence domains:
26S proteasome regulatory subunit 8 Chain: J
Molecule details ›
Chain: J
Length: 406 amino acids
Theoretical weight: 45.69 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: P62198 (Residues: 1-406; Coverage: 100%)
Gene names: Psmc5, Sug1
Sequence domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 15.4Å
Relevant EMDB volumes: EMD-3914

Quick links

Citations

67 review citations

The proteostasis network and its decline in ageing.
Hipp et al. (2019)
66 more

2 mentions without citation

In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment.
Guo et al. (2018)
1 more