› 5vgz

Electron Microscopy
4.5Å resolution

Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle

Released:
DOI: 10.2210/pdb5vgz/pdb
PDB entry 5vgz coloured by chain, front view.
PDB entry 5vgz coloured by chain, side view.
PDB entry 5vgz 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-8672

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero heptadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126189 (preferred)
Entry contents:
17 distinct polypeptide molecules
Macromolecules (17 distinct):
26S proteasome regulatory subunit 7 Chain: A
Molecule details ›
Chain: A
Length: 83 amino acids
Theoretical weight: 9.31 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P35998 (Residues: 73-155; Coverage: 19%)
Gene names: MSS1, PSMC2
Sequence domains: 26S proteasome regulatory subunit 7, OB domain
26S proteasome regulatory subunit 4 Chain: B
Molecule details ›
Chain: B
Length: 73 amino acids
Theoretical weight: 7.97 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62191 (Residues: 93-165; Coverage: 17%)
Gene name: PSMC1
Sequence domains: Proteasomal ATPase OB C-terminal domain
26S proteasome regulatory subunit 8 Chain: C
Molecule details ›
Chain: C
Length: 118 amino acids
Theoretical weight: 13.6 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62195 (Residues: 11-128; Coverage: 29%)
Gene names: PSMC5, SUG1
Sequence domains: Proteasomal ATPase OB C-terminal domain
26S proteasome regulatory subunit 6B Chain: D
Molecule details ›
Chain: D
Length: 107 amino acids
Theoretical weight: 12.34 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P43686 (Residues: 39-145; Coverage: 26%)
Gene names: MIP224, PSMC4, TBP7
Sequence domains: Proteasomal ATPase OB C-terminal domain
26S proteasome regulatory subunit 10B Chain: E
Molecule details ›
Chain: E
Length: 104 amino acids
Theoretical weight: 12.2 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P62333 (Residues: 11-114; Coverage: 27%)
Gene names: PSMC6, SUG2
Sequence domains: Proteasomal ATPase OB C-terminal domain
26S proteasome regulatory subunit 6A Chain: F
Molecule details ›
Chain: F
Length: 115 amino acids
Theoretical weight: 12.94 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P17980 (Residues: 53-167; Coverage: 26%)
Gene names: PSMC3, TBP1
Sequence domains: Proteasomal ATPase OB C-terminal domain
26S proteasome non-ATPase regulatory subunit 1 Chain: U
Molecule details ›
Chain: U
Length: 935 amino acids
Theoretical weight: 103.76 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q99460 (Residues: 1-935; Coverage: 98%)
Gene name: PSMD1
Sequence domains:
Structure domains: Leucine-rich Repeat Variant
26S proteasome non-ATPase regulatory subunit 3 Chain: V
Molecule details ›
Chain: V
Length: 488 amino acids
Theoretical weight: 55.7 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O43242 (Residues: 18-505; Coverage: 91%)
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%)
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: 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
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

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 4.5Å
Relevant EMDB volumes: EMD-8672
Expression system: Homo sapiens

Quick links

Citations

7 review citations

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

3 mentions without citation

Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle.
Lu et al. (2017)
2 more