› 3l1z

X-ray diffraction
3.17Å resolution

Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme

Released:
DOI: 10.2210/pdb3l1z/pdb
PDB entry 3l1z coloured by chain, front view.
PDB entry 3l1z coloured by chain, side view.
PDB entry 3l1z coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis for the association of human E4B U box ubiquitin ligase with E2-conjugating enzymes UbcH5c and Ubc4.
Benirschke RC, Thompson JR, Nominé Y, Wasielewski E, Juranić N, Macura S, Hatakeyama S, Nakayama KI, Botuyan MV, Mer G
Structure 18 955-65 (2010)
PMID: 20696396

Function and Biology Details

Reactions catalysed: 
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
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:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131832 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin-conjugating enzyme E2 D3 Chain: A
Molecule details ›
Chain: A
Length: 157 amino acids
Theoretical weight: 18 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61077 (Residues: 1-147; Coverage: 100%)
Gene names: UBC5C, UBCH5C, UBE2D3
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
Ubiquitin conjugation factor E4 B Chain: B
Molecule details ›
Chain: B
Length: 100 amino acids
Theoretical weight: 11.55 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O95155 (Residues: 1208-1302; Coverage: 7%)
Gene names: HDNB1, KIAA0684, UBE4B, UFD2
Sequence domains: U-box domain
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-BM
Spacegroup: P622
Unit cell:
a: 142.708Å b: 142.708Å c: 83.133Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.236 0.232 0.279
Expression system: Escherichia coli

Quick links

Citations

8 review citations

Ubiquitin Ligases: Structure, Function, and Regulation.
Zheng et al. (2017)
7 more

8 mentions without citation

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