› 2yho

X-ray diffraction
2.1Å resolution

The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor

Released:
DOI: 10.2210/pdb2yho/pdb
PDB entry 2yho coloured by chain, front view.
PDB entry 2yho coloured by chain, side view.
PDB entry 2yho coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor.
Zhang L, Fairall L, Goult BT, Calkin AC, Hong C, Millard CJ, Tontonoz P, Schwabe JW
Genes Dev 25 1262-74 (2011)
PMID: 21685362

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
(1a) S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [(E3-independent) E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-monoubiquitinyl-[(E3-independent) ubiquitin-conjugating enzyme]-L-cysteine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-156391 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 ubiquitin-protein ligase MYLIP Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 79 amino acids
Theoretical weight: 8.86 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8WY64 (Residues: 369-445; Coverage: 17%)
Gene names: BM-023, BZF1, IDOL, MYLIP, PP5242
Sequence domains: Zinc finger, C3HC4 type (RING finger)
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Ubiquitin-conjugating enzyme E2 D1 Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 149 amino acids
Theoretical weight: 16.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P51668 (Residues: 1-147; Coverage: 100%)
Gene names: SFT, UBC5A, UBCH5, UBCH5A, UBE2D1
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand ACT 9 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P21
Unit cell:
a: 57.69Å b: 137.87Å c: 63.75Å
α: 90° β: 106.39° γ: 90°
R-values:
R R work R free
0.188 0.186 0.233
Expression system: Escherichia coli

Quick links

Citations

14 review citations

Transcriptional integration of metabolism by the nuclear sterol-activated receptors LXR and FXR.
Calkin et al. (2012)
13 more

10 mentions without citation

Specificity and disease in the ubiquitin system.
Chaugule et al. (2016)
9 more