› 5h7s

X-ray diffraction
3.49Å resolution

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

Released:
DOI: 10.2210/pdb5h7s/pdb
PDB entry 5h7s coloured by chain, front view.
PDB entry 5h7s coloured by chain, side view.
PDB entry 5h7s 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

Reactions 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
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-143302 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin Chains: E, F
Molecule details ›
Chains: E, F
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family
E3 ubiquitin-protein ligase LNX Chains: B, D
Molecule details ›
Chains: B, 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)
Ubiquitin-conjugating enzyme E2 N Chains: A, C
Molecule details ›
Chains: A, C
Length: 152 amino acids
Theoretical weight: 17.13 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61088 (Residues: 1-152; Coverage: 100%)
Gene names: BLU, UBE2N
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme

Ligands and Environments

1 bound ligand:
Ligand ZN 8 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P3121
Unit cell:
a: 122.372Å b: 122.372Å c: 135.199Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.245 0.241 0.286
Expression system: Escherichia coli

Quick links

Citations

2 review citations

LNX1/LNX2 proteins: functions in neuronal signalling and beyond.
Young PW. (2018)
1 more

2 mentions without citation

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