› 7bbd

X-ray diffraction
2.2Å resolution

Crystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In complex with ubiquitin charged Ube2N (Ube2N~Ub) and Ube2V2

Released:
DOI: 10.2210/pdb7bbd/pdb
PDB entry 7bbd coloured by chain, front view.
PDB entry 7bbd coloured by chain, side view.
PDB entry 7bbd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
RING domains act as both substrate and enzyme in a catalytic arrangement to drive self-anchored ubiquitination.
Kiss L, Clift D, Renner N, Neuhaus D, James LC
OpenAccess logo Nat Commun 12 1220 (2021)
PMID: 33619271

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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143229 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
E3 ubiquitin-protein ligase TRIM21; Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 164 amino acids
Theoretical weight: 18.38 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P0CG47 (Residues: 153-226; Coverage: 32%)
  • Canonical: P19474 (Residues: 1-85; Coverage: 18%)
Gene names: RNF81, RO52, SSA1, TRIM21, UBB
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 BL21(DE3)
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
Ubiquitin-conjugating enzyme E2 variant 2 Chain: A
Molecule details ›
Chain: A
Length: 150 amino acids
Theoretical weight: 16.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q15819 (Residues: 1-145; Coverage: 100%)
Gene names: MMS2, UBE2V2, UEV2
Sequence domains: Ubiquitin-conjugating enzyme
Ubiquitin-conjugating enzyme E2 N Chain: C
Molecule details ›
Chain: C
Length: 153 amino acids
Theoretical weight: 17.18 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P61088 (Residues: 1-152; Coverage: 100%)
Gene names: BLU, UBE2N
Sequence domains: Ubiquitin-conjugating enzyme

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: C2
Unit cell:
a: 99.15Å b: 108.36Å c: 75.14Å
α: 90° β: 104.99° γ: 90°
R-values:
R R work R free
0.224 0.222 0.252
Expression systems:
  • Escherichia coli BL21
  • Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

TRIM21/Ro52 - Roles in Innate Immunity and Autoimmune Disease.
Jones et al. (2021)
1 more

3 mentions without citation

RING domains act as both substrate and enzyme in a catalytic arrangement to drive self-anchored ubiquitination.
Kiss et al. (2021)
2 more