› 5v1z

X-ray diffraction
2Å resolution

Crystal structure of the RPN13 PRU-RPN2 (932-953)-ubiquitin complex

Released:
DOI: 10.2210/pdb5v1z/pdb
PDB entry 5v1z coloured by chain, front view.
PDB entry 5v1z coloured by chain, side view.
PDB entry 5v1z coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure and energetics of pairwise interactions between proteasome subunits RPN2, RPN13, and ubiquitin clarify a substrate recruitment mechanism.
VanderLinden RT, Hemmis CW, Yao T, Robinson H, Hill CP
J Biol Chem 292 9493-9504 (2017)
PMID: 28442575

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-143267 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Proteasomal ubiquitin receptor ADRM1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 115 amino acids
Theoretical weight: 13.48 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q16186 (Residues: 19-132; Coverage: 28%)
Gene names: ADRM1, GP110
Sequence domains: Proteasome complex subunit Rpn13, Pru domain
Structure domains: Proteasomal ubiquitin receptor Rpn13/ADRM1
Ubiquitin Chains: C, D
Molecule details ›
Chains: C, D
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family
26S proteasome non-ATPase regulatory subunit 1 Chains: E, F
Molecule details ›
Chains: E, F
Length: 22 amino acids
Theoretical weight: 2.62 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q99460 (Residues: 932-953; Coverage: 2%)
Gene name: PSMD1

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: P31
Unit cell:
a: 100.852Å b: 100.852Å c: 37.571Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.155 0.146 0.182
Expression system: Escherichia coli BL21

Quick links

Citations

6 review citations

Proteasome interaction with ubiquitinated substrates: from mechanisms to therapies.
Chen et al. (2021)
5 more

2 mentions without citation

Structure and Function of the 26S Proteasome.
Bard et al. (2018)
1 more