› 5vhf

Electron Microscopy
5.7Å resolution

Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle

Released:
DOI: 10.2210/pdb5vhf/pdb
PDB entry 5vhf coloured by chain, front view.
PDB entry 5vhf coloured by chain, side view.
PDB entry 5vhf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle.
Lu Y, Wu J, Dong Y, Chen S, Sun S, Ma YB, Ouyang Q, Finley D, Kirschner MW, Mao Y
Mol Cell 67 322-333.e6 (2017)
PMID: 28689658
Related structures: EMD-8674

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero nonadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-517162 (preferred)
Entry contents:
19 distinct polypeptide molecules
Macromolecules (19 distinct):
26S proteasome non-ATPase regulatory subunit 10 Chain: G
Molecule details ›
Chain: G
Length: 223 amino acids
Theoretical weight: 24.14 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O75832 (Residues: 4-226; Coverage: 99%)
Gene name: PSMD10
Sequence domains: Ankyrin repeats (3 copies)
26S proteasome regulatory subunit 7 Chain: A
Molecule details ›
Chain: A
Length: 352 amino acids
Theoretical weight: 39.4 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P35998 (Residues: 73-424; Coverage: 81%)
Gene names: MSS1, PSMC2
Sequence domains:
26S proteasome regulatory subunit 4 Chain: B
Molecule details ›
Chain: B
Length: 340 amino acids
Theoretical weight: 37.97 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62191 (Residues: 93-432; Coverage: 77%)
Gene name: PSMC1
Sequence domains:
26S proteasome regulatory subunit 8 Chain: C
Molecule details ›
Chain: C
Length: 385 amino acids
Theoretical weight: 43.2 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62195 (Residues: 11-395; Coverage: 95%)
Gene names: PSMC5, SUG1
Sequence domains:
26S proteasome regulatory subunit 6B Chain: D
Molecule details ›
Chain: D
Length: 368 amino acids
Theoretical weight: 41.72 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P43686 (Residues: 39-406; Coverage: 88%)
Gene names: MIP224, PSMC4, TBP7
Sequence domains:
26S proteasome regulatory subunit 10B Chain: E
Molecule details ›
Chain: E
Length: 379 amino acids
Theoretical weight: 43.11 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62333 (Residues: 11-389; Coverage: 97%)
Gene names: PSMC6, SUG2
Sequence domains:
26S proteasome regulatory subunit 6A Chain: F
Molecule details ›
Chain: F
Length: 380 amino acids
Theoretical weight: 42.47 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P17980 (Residues: 53-432; Coverage: 87%)
Gene names: PSMC3, TBP1
Sequence domains:
26S proteasome non-ATPase regulatory subunit 1 Chain: U
Molecule details ›
Chain: U
Length: 841 amino acids
Theoretical weight: 93.31 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q99460 (Residues: 95-935; Coverage: 88%)
Gene name: PSMD1
Sequence domains:
26S proteasome non-ATPase regulatory subunit 3 Chain: V
Molecule details ›
Chain: V
Length: 183 amino acids
Theoretical weight: 21.05 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O43242 (Residues: 323-505; Coverage: 34%)
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: 385 amino acids
Theoretical weight: 43.43 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O00231 (Residues: 38-422; Coverage: 91%)
  • Best match: O00231-2 (Residues: 38-423)
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: 374 amino acids
Theoretical weight: 42.73 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9UNM6 (Residues: 3-376; Coverage: 100%)
Gene name: PSMD13
Sequence domains:
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: 136 amino acids
Theoretical weight: 15.73 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P48556 (Residues: 215-350; Coverage: 39%)
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
Expression system: 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: 848 amino acids
Theoretical weight: 93.79 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q13200 (Residues: 6-853; Coverage: 93%)
Gene names: PSMD2, TRAP2
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 5.7Å
Relevant EMDB volumes: EMD-8674
Expression system: Homo sapiens

Quick links

Citations

6 review citations

Cryo-EM for Small Molecules Discovery, Design, Understanding, and Application.
Scapin et al. (2018)
5 more

3 mentions without citation

Wiggle and Shake: Managing and Exploiting Conformational Dynamics during Proteasome Biogenesis.
Betancourt et al. (2023)
2 more