› 5tte

X-ray diffraction
3.5Å resolution

Crystal Structure of an RBR E3 ubiquitin ligase in complex with an E2-Ub thioester intermediate mimic

Released:
DOI: 10.2210/pdb5tte/pdb
PDB entry 5tte coloured by chain, front view.
PDB entry 5tte coloured by chain, side view.
PDB entry 5tte coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into the mechanism and E2 specificity of the RBR E3 ubiquitin ligase HHARI.
Yuan L, Lv Z, Atkison JH, Olsen SK
Nat Commun 8 211 (2017)
PMID: 28790309

Function and Biology Details

Reactions catalysed: 
(1a) [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [RBR-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [RBR-type E3 ubiquitin transferase]-S-ubiquitinyl-L-cysteine
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 trimer (preferred)
PDBe Complex ID:
PDB-CPX-159271 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
E3 ubiquitin-protein ligase ARIH1 Chain: B
Molecule details ›
Chain: B
Length: 558 amino acids
Theoretical weight: 64.28 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9Y4X5 (Residues: 1-557; Coverage: 100%)
Gene names: ARI, ARIH1, HUSSY-27, MOP6, UBCH7BP
Sequence domains:
Structure domains: Four Helix Bundle (Hemerythrin (Met), subunit A)
Ubiquitin-conjugating enzyme E2 L3 Chain: E
Molecule details ›
Chain: E
Length: 167 amino acids
Theoretical weight: 19.43 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P68036 (Residues: 1-154; Coverage: 100%)
Gene names: UBCE7, UBCH7, UBE2L3
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
Ubiquitin Chain: F
Molecule details ›
Chain: F
Length: 86 amino acids
Theoretical weight: 9.98 KDa
Source organism: Triticum aestivum
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P69326 (Residues: 1-76; Coverage: 99%)
Sequence domains: Ubiquitin family

Ligands and Environments

1 bound ligand:
Ligand ZN 6 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P6522
Unit cell:
a: 154.234Å b: 154.234Å c: 285.501Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.228 0.226 0.252
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 review citations

PROTAC targeted protein degraders: the past is prologue.
Békés et al. (2022)
6 more

8 mentions without citation

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