› 6n13

Solution NMR

UbcH7-Ub Complex with R0RBR Parkin and phosphoubiquitin

Released:
DOI: 10.2210/pdb6n13/pdb
PDB entry 6n13 coloured by chain, ensemble of 10 models, front view.
PDB entry 6n13 coloured by chain, ensemble of 10 models, side view.
PDB entry 6n13 coloured by chain, ensemble of 10 models, top view.
Source organism: Homo sapiens
Primary publication:
Synergistic recruitment of UbcH7~Ub and phosphorylated Ubl domain triggers parkin activation.
Condos TE, Dunkerley KM, Freeman EA, Barber KR, Aguirre JD, Chaugule VK, Xiao Y, Konermann L, Walden H, Shaw GS
EMBO J 37 (2018)
PMID: 30446597

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 tetramer (preferred)
PDBe Complex ID:
PDB-CPX-129928 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
E3 ubiquitin-protein ligase parkin Chain: B
Molecule details ›
Chain: B
Length: 322 amino acids
Theoretical weight: 36.05 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60260 (Residues: 144-465; Coverage: 69%)
Gene names: PARK2, PRKN
Sequence domains:
Ubiquitin Chain: D
Molecule details ›
Chain: D
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
Ubiquitin-conjugating enzyme E2 L3 Chain: C
Molecule details ›
Chain: C
Length: 156 amino acids
Theoretical weight: 18.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
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: A
Molecule details ›
Chain: A
Length: 76 amino acids
Theoretical weight: 8.66 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family

Ligands and Environments

1 bound ligand:
Ligand ZN 8 x ZN
1 modified residue:
Ligand SEP 1 x SEP

Experiments and Validation Details

Entry percentile scores
Chemical shift assignment: 5%
Refinement method: simulated annealing
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Post-translational regulation of ubiquitin signaling.
Song et al. (2019)
5 more

6 mentions without citation

Synergistic recruitment of UbcH7~Ub and phosphorylated Ubl domain triggers parkin activation.
Condos et al. (2018)
5 more