› 7ojx

X-ray diffraction
2.4Å resolution

E2 UBE2K covalently linked to donor Ub, acceptor di-Ub, and RING E3 primed for K48-linked Ub chain synthesis

Released:
DOI: 10.2210/pdb7ojx/pdb
PDB entry 7ojx coloured by chain, front view.
PDB entry 7ojx coloured by chain, side view.
PDB entry 7ojx coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of UBE2K-Ub/E3/polyUb reveals mechanisms of K48-linked Ub chain extension.
Nakasone MA, Majorek KA, Gabrielsen M, Sibbet GJ, Smith BO, Huang DT
OpenAccess logo Nat Chem Biol 18 422-431 (2022)
PMID: 35027744

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
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-143234 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
E3 ubiquitin-protein ligase RNF38 Chain: A
Molecule details ›
Chain: A
Length: 79 amino acids
Theoretical weight: 9.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9H0F5 (Residues: 439-515; Coverage: 15%)
Gene name: RNF38
Sequence domains: Ring finger domain
Ubiquitin-conjugating enzyme E2 K Chain: B
Molecule details ›
Chain: B
Length: 202 amino acids
Theoretical weight: 22.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P61086 (Residues: 1-200; Coverage: 100%)
Gene names: HIP2, LIG, UBE2K
Sequence domains:
Ubiquitin Chain: C
Molecule details ›
Chain: C
Length: 79 amino acids
Theoretical weight: 8.78 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family
Ubiquitin Chain: D
Molecule details ›
Chain: D
Length: 76 amino acids
Theoretical weight: 8.55 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family
Ubiquitin Chain: E
Molecule details ›
Chain: E
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand ME7 1 x ME7
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P3121
Unit cell:
a: 85.835Å b: 85.835Å c: 167.354Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.19 0.188 0.236
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Protein ubiquitination in T cell development.
Zhong et al. (2022)
1 more

2 mentions without citation

Tracking of Ubiquitin Signaling through 3.5 Billion Years of Combinatorial Conjugation.
Kaminskaya et al. (2024)
1 more