› 9e8l

Electron Microscopy
3.59Å resolution

Nub1/Fat10-processing human 26S proteasome bound to Txnl1 with Rpt4 at top of spiral staircase

Released:
DOI: 10.2210/pdb9e8l/pdb
PDB entry 9e8l coloured by chain, front view.
PDB entry 9e8l coloured by chain, side view.
PDB entry 9e8l coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural landscape of AAA+ ATPase motor states in the substrate-degrading human 26S proteasome reveals conformation-specific binding of TXNL1.
Arkinson C, Gee CL, Zhang Z, Dong KC, Martin A
bioRxiv (2024)
PMID: 39574680
Related structures: EMD-47724

Function and Biology Details

Reaction catalysed: 
Cleavage of peptide bonds with very broad specificity.
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero 28-mer (preferred)
PDBe Complex ID:
PDB-CPX-281391 (preferred)
Entry contents:
28 distinct polypeptide molecules
Macromolecules (28 distinct):
26S proteasome regulatory subunit 7 Chain: A
Molecule details ›
Chain: A
Length: 433 amino acids
Theoretical weight: 48.7 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P35998 (Residues: 1-433; Coverage: 100%)
Gene names: MSS1, PSMC2
Sequence domains:
26S proteasome regulatory subunit 4 Chain: B
Molecule details ›
Chain: B
Length: 440 amino acids
Theoretical weight: 49.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62191 (Residues: 1-440; Coverage: 100%)
Gene name: PSMC1
Sequence domains:
26S proteasome regulatory subunit 8 Chain: C
Molecule details ›
Chain: C
Length: 406 amino acids
Theoretical weight: 45.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62195 (Residues: 1-406; Coverage: 100%)
Gene names: PSMC5, SUG1
Sequence domains:
26S proteasome regulatory subunit 6B Chain: D
Molecule details ›
Chain: D
Length: 418 amino acids
Theoretical weight: 47.43 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P43686 (Residues: 1-418; Coverage: 100%)
Gene names: MIP224, PSMC4, TBP7
Sequence domains:
26S proteasome regulatory subunit 10B Chain: E
Molecule details ›
Chain: E
Length: 389 amino acids
Theoretical weight: 44.24 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62333 (Residues: 1-389; Coverage: 100%)
Gene names: PSMC6, SUG2
Sequence domains:
26S proteasome regulatory subunit 6A Chain: F
Molecule details ›
Chain: F
Length: 439 amino acids
Theoretical weight: 49.27 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P17980 (Residues: 1-439; Coverage: 100%)
Gene names: PSMC3, TBP1
Sequence domains:
Proteasome subunit alpha type-6 Chain: G
Molecule details ›
Chain: G
Length: 246 amino acids
Theoretical weight: 27.43 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P60900 (Residues: 1-246; Coverage: 100%)
Gene names: PROS27, PSMA6
Sequence domains:
Proteasome subunit alpha type-2 Chain: H
Molecule details ›
Chain: H
Length: 234 amino acids
Theoretical weight: 25.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25787 (Residues: 1-234; Coverage: 100%)
Gene names: HC3, PSC3, PSMA2
Sequence domains:
Proteasome subunit alpha type-4 Chain: I
Molecule details ›
Chain: I
Length: 261 amino acids
Theoretical weight: 29.53 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25789 (Residues: 1-261; Coverage: 100%)
Gene names: HC9, PSC9, PSMA4
Sequence domains:
Proteasome subunit alpha type-7 Chain: J
Molecule details ›
Chain: J
Length: 248 amino acids
Theoretical weight: 27.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O14818 (Residues: 1-248; Coverage: 100%)
Gene names: HSPC, PSMA7
Sequence domains:
Proteasome subunit alpha type-5 Chain: K
Molecule details ›
Chain: K
Length: 241 amino acids
Theoretical weight: 26.44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P28066 (Residues: 1-241; Coverage: 100%)
Gene name: PSMA5
Sequence domains:
Proteasome subunit alpha type-1 Chain: L
Molecule details ›
Chain: L
Length: 263 amino acids
Theoretical weight: 29.6 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25786 (Residues: 1-263; Coverage: 100%)
Gene names: HC2, NU, PROS30, PSC2, PSMA1
Sequence domains:
Proteasome subunit alpha type-3 Chain: M
Molecule details ›
Chain: M
Length: 255 amino acids
Theoretical weight: 28.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25788 (Residues: 1-255; Coverage: 100%)
Gene names: HC8, PSC8, PSMA3
Sequence domains:
26S proteasome non-ATPase regulatory subunit 1 Chain: U
Molecule details ›
Chain: U
Length: 953 amino acids
Theoretical weight: 105.96 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q99460 (Residues: 1-953; Coverage: 100%)
Gene name: PSMD1
Sequence domains:
26S proteasome non-ATPase regulatory subunit 3 Chain: V
Molecule details ›
Chain: V
Length: 534 amino acids
Theoretical weight: 61.07 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43242 (Residues: 1-534; Coverage: 100%)
Gene name: PSMD3
Sequence domains:
26S proteasome non-ATPase regulatory subunit 12 Chain: W
Molecule details ›
Chain: W
Length: 456 amino acids
Theoretical weight: 52.98 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O00232 (Residues: 1-456; Coverage: 100%)
Gene name: PSMD12
Sequence domains:
26S proteasome non-ATPase regulatory subunit 11 Chain: X
Molecule details ›
Chain: X
Length: 422 amino acids
Theoretical weight: 47.53 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O00231 (Residues: 1-422; Coverage: 100%)
  • Best match: O00231-2 (Residues: 1-423)
Gene name: PSMD11
Sequence domains:
26S proteasome non-ATPase regulatory subunit 6 Chain: Y
Molecule details ›
Chain: Y
Length: 389 amino acids
Theoretical weight: 45.59 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15008 (Residues: 1-389; Coverage: 100%)
Gene names: KIAA0107, PFAAP4, PSMD6
Sequence domains:
26S proteasome non-ATPase regulatory subunit 7 Chain: Z
Molecule details ›
Chain: Z
Length: 324 amino acids
Theoretical weight: 37.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P51665 (Residues: 1-324; Coverage: 100%)
Gene names: MOV34L, PSMD7
Sequence domains:
26S proteasome non-ATPase regulatory subunit 13 Chain: a
Molecule details ›
Chain: a
Length: 376 amino acids
Theoretical weight: 43 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UNM6 (Residues: 1-376; Coverage: 100%)
Gene name: PSMD13
Sequence domains:
26S proteasome non-ATPase regulatory subunit 4 Chain: b
Molecule details ›
Chain: b
Length: 377 amino acids
Theoretical weight: 40.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P55036 (Residues: 1-377; Coverage: 100%)
Gene names: MCB1, PSMD4
Sequence domains:
26S proteasome non-ATPase regulatory subunit 14 Chain: c
Molecule details ›
Chain: c
Length: 424 amino acids
Theoretical weight: 46.94 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O00487 (Residues: 1-310; Coverage: 100%)
Gene names: POH1, PSMD14
Sequence domains: JAB1/Mov34/MPN/PAD-1 ubiquitin protease
26S proteasome non-ATPase regulatory subunit 8 Chain: d
Molecule details ›
Chain: d
Length: 350 amino acids
Theoretical weight: 39.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P48556 (Residues: 1-350; Coverage: 100%)
Gene name: PSMD8
Sequence domains: CSN8/PSMD8/EIF3K family
26S proteasome complex subunit SEM1 Chain: e
Molecule details ›
Chain: e
Length: 70 amino acids
Theoretical weight: 8.28 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P60896 (Residues: 1-70; Coverage: 100%)
Gene names: C7orf76, DSS1, SEM1, SHFDG1, SHFM1
Sequence domains: DSS1/SEM1 family
26S proteasome non-ATPase regulatory subunit 2 Chain: f
Molecule details ›
Chain: f
Length: 908 amino acids
Theoretical weight: 100.31 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13200 (Residues: 1-908; Coverage: 100%)
Gene names: PSMD2, TRAP2
Sequence domains:
NEDD8 ultimate buster 1 Chain: g
Molecule details ›
Chain: g
Length: 601 amino acids
Theoretical weight: 69.22 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9Y5A7 (Residues: 1-615; Coverage: 98%)
  • Best match: Q9Y5A7-2 (Residues: 1-601)
Gene names: NUB1, NYREN18
Sequence domains:
Thioredoxin-like protein 1 Chain: u
Molecule details ›
Chain: u
Length: 289 amino acids
Theoretical weight: 32.28 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O43396 (Residues: 1-289; Coverage: 100%)
Gene names: TRP32, TXL, TXNL, TXNL1
Sequence domains:
substrate peptide Chain: v
Molecule details ›
Chain: v
Length: 14 amino acids
Theoretical weight: 1.21 KDa
Source organism: Homo sapiens

Ligands and Environments

4 bound ligands:
Ligand ADP 4 x ADP
Ligand MG 3 x MG
Ligand ATP 2 x ATP
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.59Å
Relevant EMDB volumes: EMD-47724
Expression systems:
  • Homo sapiens
  • Escherichia coli BL21(DE3)

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