6t7f

X-ray diffraction
2.58Å resolution

RCR E3 ligase E2-Ubiquitin transthiolation intermediate

Released:

Function and Biology Details

Reactions catalysed:
(1a) [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [RCR-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [RCR-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
(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:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
E3 ubiquitin-protein ligase MYCBP2 Chain: A
Molecule details ›
Chain: A
Length: 261 amino acids
Theoretical weight: 29.41 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O75592 (Residues: 4423-4678; Coverage: 6%)
Gene names: KIAA0916, MYCBP2, PAM
Sequence domains: Ring finger domain
Ubiquitin-conjugating enzyme E2 D3 Chain: B
Molecule details ›
Chain: B
Length: 150 amino acids
Theoretical weight: 16.9 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61077 (Residues: 2-147; Coverage: 99%)
Gene names: UBC5C, UBCH5C, UBE2D3
Sequence domains: Ubiquitin-conjugating enzyme
Ubiquitin Chain: C
Molecule details ›
Chain: C
Length: 73 amino acids
Theoretical weight: 8.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-681; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family

Ligands and Environments

2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: R32
Unit cell:
a: 179.008Å b: 179.008Å c: 87.276Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.198 0.195 0.256
Expression system: Escherichia coli