› 5h7r

X-ray diffraction
1.7Å resolution

Structural basis of the flanking zinc-finger motifs crucial for the E3 ligase activity of the LNX1 RING domain

Released:
DOI: 10.2210/pdb5h7r/pdb
PDB entry 5h7r coloured by chain, front view.
PDB entry 5h7r coloured by chain, side view.
PDB entry 5h7r coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of LNX1:Ubc13~Ubiquitin Complex Reveals the Role of Additional Motifs for the E3 Ligase Activity of LNX1.
Nayak D, Sivaraman J
J Mol Biol 430 1173-1188 (2018)
PMID: 29496391

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-186172 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
E3 ubiquitin-protein ligase LNX Chain: D
Molecule details ›
Chain: D
Length: 128 amino acids
Theoretical weight: 14.63 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8TBB1 (Residues: 11-138; Coverage: 18%)
Gene names: LNX, LNX1, PDZRN2, UNQ574/PRO1136
Sequence domains: Zinc finger, C3HC4 type (RING finger)
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P6222
Unit cell:
a: 92.375Å b: 92.375Å c: 84.41Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.182 0.178 0.215
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Structural basis of generic versus specific E2-RING E3 interactions in protein ubiquitination.
Gundogdu et al. (2019)
2 more