› 5vfq

Electron Microscopy
4.2Å resolution

Nucleotide-driven Triple-state Remodeling of the AAA-ATPase Channel in the Activated Human 26S Proteasome

Released:
DOI: 10.2210/pdb5vfq/pdb
PDB entry 5vfq coloured by chain, front view.
PDB entry 5vfq coloured by chain, side view.
PDB entry 5vfq coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome.
Zhu Y, Wang WL, Yu D, Ouyang Q, Lu Y, Mao Y
Nat Commun 9 1360 (2018)
PMID: 29636472
Related structures: EMD-8664

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 46-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126184 (preferred)
Entry contents:
32 distinct polypeptide molecules
Macromolecules (32 distinct):
Proteasome subunit alpha type-6 Chains: G, g
Molecule details ›
Chains: G, g
Length: 240 amino acids
Theoretical weight: 26.73 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P60900 (Residues: 5-244; Coverage: 98%)
Gene names: PROS27, PSMA6
Sequence domains:
Proteasome subunit alpha type-2 Chains: H, h
Molecule details ›
Chains: H, h
Length: 232 amino acids
Theoretical weight: 25.73 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P25787 (Residues: 3-234; Coverage: 99%)
Gene names: HC3, PSC3, PSMA2
Sequence domains:
Proteasome subunit alpha type-4 Chains: I, i
Molecule details ›
Chains: I, i
Length: 250 amino acids
Theoretical weight: 28.12 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P25789 (Residues: 2-251; Coverage: 96%)
Gene names: HC9, PSC9, PSMA4
Sequence domains:
Proteasome subunit alpha type-7 Chains: J, j
Molecule details ›
Chains: J, j
Length: 243 amino acids
Theoretical weight: 27.38 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O14818 (Residues: 2-244; Coverage: 98%)
Gene names: HSPC, PSMA7
Sequence domains:
Proteasome subunit alpha type-5 Chains: K, k
Molecule details ›
Chains: K, k
Length: 234 amino acids
Theoretical weight: 25.57 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P28066 (Residues: 8-241; Coverage: 97%)
Gene name: PSMA5
Sequence domains:
Proteasome subunit alpha type-1 Chains: L, l
Molecule details ›
Chains: L, l
Length: 238 amino acids
Theoretical weight: 26.73 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P25786 (Residues: 4-241; Coverage: 91%)
Gene names: HC2, NU, PROS30, PSC2, PSMA1
Sequence domains:
Proteasome subunit alpha type-3 Chains: M, m
Molecule details ›
Chains: M, m
Length: 245 amino acids
Theoretical weight: 27.29 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P25788 (Residues: 2-246; Coverage: 96%)
Gene names: HC8, PSC8, PSMA3
Sequence domains:
Proteasome subunit beta type-6 Chains: N, n
Molecule details ›
Chains: N, n
Length: 191 amino acids
Theoretical weight: 20.47 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P28072 (Residues: 35-225; Coverage: 80%)
Gene names: LMPY, PSMB6, Y
Sequence domains: Proteasome subunit
Proteasome subunit beta type-7 Chains: O, o
Molecule details ›
Chains: O, o
Length: 220 amino acids
Theoretical weight: 23.75 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q99436 (Residues: 44-263; Coverage: 79%)
Gene names: PSMB7, Z
Sequence domains:
Proteasome subunit beta type-3 Chains: P, p
Molecule details ›
Chains: P, p
Length: 204 amino acids
Theoretical weight: 22.84 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P49720 (Residues: 2-205; Coverage: 100%)
Gene name: PSMB3
Sequence domains: Proteasome subunit
Proteasome subunit beta type-2 Chains: Q, q
Molecule details ›
Chains: Q, q
Length: 199 amino acids
Theoretical weight: 22.72 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P49721 (Residues: 1-199; Coverage: 99%)
Gene name: PSMB2
Sequence domains: Proteasome subunit
Proteasome subunit beta type-5 Chains: R, r
Molecule details ›
Chains: R, r
Length: 201 amino acids
Theoretical weight: 22.2 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P28074 (Residues: 60-260; Coverage: 76%)
Gene names: LMPX, MB1, PSMB5, X
Sequence domains: Proteasome subunit
Proteasome subunit beta type-1 Chains: S, s
Molecule details ›
Chains: S, s
Length: 213 amino acids
Theoretical weight: 23.58 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P20618 (Residues: 29-241; Coverage: 88%)
Gene names: PSC5, PSMB1
Sequence domains: Proteasome subunit
Proteasome subunit beta type-4 Chains: T, t
Molecule details ›
Chains: T, t
Length: 215 amino acids
Theoretical weight: 23.99 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P28070 (Residues: 46-260; Coverage: 81%)
Gene names: PROS26, PSMB4
Sequence domains: Proteasome subunit
26S proteasome non-ATPase regulatory subunit 1 Chain: U
Molecule details ›
Chain: U
Length: 911 amino acids
Theoretical weight: 101.26 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q99460 (Residues: 7-917; Coverage: 96%)
Gene name: PSMD1
Sequence domains:
26S proteasome non-ATPase regulatory subunit 3 Chain: V
Molecule details ›
Chain: V
Length: 480 amino acids
Theoretical weight: 54.76 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O43242 (Residues: 18-497; Coverage: 90%)
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
Expression system: 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: 380 amino acids
Theoretical weight: 42.87 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O00231 (Residues: 43-422; Coverage: 90%)
Gene name: PSMD11
Sequence domains:
26S proteasome non-ATPase regulatory subunit 6 Chain: Y
Molecule details ›
Chain: Y
Length: 378 amino acids
Theoretical weight: 44.34 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q15008 (Residues: 12-389; Coverage: 97%)
Gene names: KIAA0107, PFAAP4, PSMD6
Sequence domains:
26S proteasome non-ATPase regulatory subunit 7 Chain: Z
Molecule details ›
Chain: Z
Length: 286 amino acids
Theoretical weight: 32.38 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P51665 (Residues: 5-290; Coverage: 88%)
Gene names: MOV34L, PSMD7
Sequence domains:
26S proteasome non-ATPase regulatory subunit 13 Chain: a
Molecule details ›
Chain: a
Length: 373 amino acids
Theoretical weight: 42.62 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9UNM6 (Residues: 4-376; Coverage: 99%)
Gene name: PSMD13
Sequence domains: PCI domain
26S proteasome non-ATPase regulatory subunit 4 Chain: b
Molecule details ›
Chain: b
Length: 191 amino acids
Theoretical weight: 20.87 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P55036 (Residues: 1-191; Coverage: 51%)
Gene names: MCB1, PSMD4
Sequence domains: von Willebrand factor type A domain
26S proteasome non-ATPase regulatory subunit 14 Chain: c
Molecule details ›
Chain: c
Length: 287 amino acids
Theoretical weight: 32.33 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O00487 (Residues: 24-310; Coverage: 93%)
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: 257 amino acids
Theoretical weight: 30.04 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P48556 (Residues: 94-350; Coverage: 73%)
Gene name: PSMD8
Sequence domains: CSN8/PSMD8/EIF3K family
Sem1 Chain: e
Molecule details ›
Chain: e
Length: 70 amino acids
Theoretical weight: 8.28 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
26S proteasome regulatory subunit 7 Chain: A
Molecule details ›
Chain: A
Length: 399 amino acids
Theoretical weight: 44.82 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P35998 (Residues: 35-433; Coverage: 92%)
Gene names: MSS1, PSMC2
Sequence domains:
26S proteasome regulatory subunit 4 Chain: B
Molecule details ›
Chain: B
Length: 389 amino acids
Theoretical weight: 43.89 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62191 (Residues: 52-440; Coverage: 88%)
Gene name: PSMC1
Sequence domains:
26S proteasome regulatory subunit 8 Chain: C
Molecule details ›
Chain: C
Length: 392 amino acids
Theoretical weight: 44.03 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62195 (Residues: 11-402; Coverage: 97%)
Gene names: PSMC5, SUG1
Sequence domains:
26S proteasome regulatory subunit 6B Chain: D
Molecule details ›
Chain: D
Length: 380 amino acids
Theoretical weight: 43.3 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P43686 (Residues: 39-418; Coverage: 91%)
Gene names: MIP224, PSMC4, TBP7
Sequence domains:
26S proteasome regulatory subunit 10B Chain: E
Molecule details ›
Chain: E
Length: 375 amino acids
Theoretical weight: 42.55 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62333 (Residues: 15-389; Coverage: 96%)
Gene names: PSMC6, SUG2
Sequence domains:
26S proteasome regulatory subunit 6A Chain: F
Molecule details ›
Chain: F
Length: 396 amino acids
Theoretical weight: 44.38 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P17980 (Residues: 44-439; Coverage: 90%)
Gene names: PSMC3, TBP1
Sequence domains:
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
Expression system: Homo sapiens
UniProt:
  • Canonical: Q13200 (Residues: 1-908; Coverage: 100%)
Gene names: PSMD2, TRAP2
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand AGS 4 x AGS
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.2Å
Relevant EMDB volumes: EMD-8664
Expression system: Homo sapiens

Quick links

Citations

14 review citations

Structure, Dynamics and Function of the 26S Proteasome.
Mao Y. (2021)
13 more

3 mentions without citation

Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome.
Zhu et al. (2018)
2 more