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X-ray diffraction
1.8Å resolution

Crystal structure of the KH1 domain of human RNA-binding E3 ubiquitin-protein ligase MEX-3C complex with RNA

Released:
DOI: 10.2210/pdb5www/pdb
PDB entry 5www coloured by chain, front view.
PDB entry 5www coloured by chain, side view.
PDB entry 5www coloured by chain, top view.
Source organisms:
Primary publication:
The human RNA-binding protein and E3 ligase MEX-3C binds the MEX-3-recognition element (MRE) motif with high affinity.
Yang L, Wang C, Li F, Zhang J, Nayab A, Wu J, Shi Y, Gong Q
J Biol Chem 292 16221-16234 (2017)
PMID: 28808060

Function and Biology Details

Reaction 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
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-178347 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
RNA-binding E3 ubiquitin-protein ligase MEX3C Chain: A
Molecule details ›
Chain: A
Length: 94 amino acids
Theoretical weight: 10.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5U5Q3 (Residues: 221-306; Coverage: 13%)
Gene names: BM-013, MEX3C, RKHD2, RNF194
Sequence domains: KH domain
Structure domains: K Homology domain, type 1
RNA (5'-R(*GP*UP*UP*UP*AP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 6 nucleotides
Theoretical weight: 1.89 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P62
Unit cell:
a: 76.366Å b: 76.366Å c: 36.392Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.174 0.172 0.209
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms.
Corley et al. (2020)
3 more

4 mentions without citation

Oncogenic Potential of the Dual-Function Protein MEX3A.
Lederer et al. (2021)
3 more