› 5vzw

X-ray diffraction
2.28Å resolution

TRIM23 RING domain in complex with UbcH5-Ub

Released:
DOI: 10.2210/pdb5vzw/pdb
PDB entry 5vzw coloured by chain, front view.
PDB entry 5vzw coloured by chain, side view.
PDB entry 5vzw coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure and catalytic activation of the TRIM23 RING E3 ubiquitin ligase.
Dawidziak DM, Sanchez JG, Wagner JM, Ganser-Pornillos BK, Pornillos O
Proteins 85 1957-1961 (2017)
PMID: 28681414

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 hexamer (preferred)
PDBe Complex ID:
PDB-CPX-143298 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin-conjugating enzyme E2 D2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 147 amino acids
Theoretical weight: 16.85 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62837 (Residues: 1-147; Coverage: 100%)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
Ubiquitin Chains: C, D
Molecule details ›
Chains: C, D
Length: 79 amino acids
Theoretical weight: 8.86 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family
E3 ubiquitin-protein ligase TRIM23 Chains: F, G
Molecule details ›
Chains: F, G
Length: 123 amino acids
Theoretical weight: 13.11 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P36406 (Residues: 1-123; Coverage: 21%)
Gene names: ARD1, ARFD1, RNF46, TRIM23
Sequence domains: RING-type zinc-finger

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 52.83Å b: 109.355Å c: 122.963Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.208 0.237
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli

Quick links

Citations

3 review citations

The TRIMendous Role of TRIMs in Virus-Host Interactions.
van Tol et al. (2017)
2 more

6 mentions without citation

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