Structural basis of pre-let-7 miRNA recognition by the zinc knuckles of pluripotency factor Lin28

Nat Struct Mol Biol. 2011 Dec 11;19(1):84-9. doi: 10.1038/nsmb.2202.


Lin28 inhibits the biogenesis of let-7 miRNAs through a direct interaction with the terminal loop of pre-let-7. This interaction requires the zinc-knuckle domains of Lin28. We show that the zinc knuckle domains of Lin28 are sufficient to provide binding selectivity for pre-let-7 miRNAs and present the NMR structure of human Lin28 zinc knuckles bound to the short sequence 5'-AGGAGAU-3'. The structure reveals that each zinc knuckle recognizes an AG dinucleotide separated by a single nucleotide spacer. This defines a new 5'-NGNNG-3' consensus motif that explains how Lin28 selectively recognizes pre-let-7 family members. Binding assays in cell lysates and functional assays in cultured cells demonstrate that the interactions observed in the solution structure also occur between the full-length protein and members of the pre-let-7 family. The consensus sequence explains several seemingly disparate previously published observations on the binding properties of Lin28.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Binding Sites / genetics
  • Binding, Competitive
  • Calorimetry
  • Cell Line, Tumor
  • HeLa Cells
  • Humans
  • Magnetic Resonance Spectroscopy
  • MicroRNAs / chemistry*
  • MicroRNAs / genetics
  • MicroRNAs / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Mutation
  • Nucleic Acid Conformation*
  • Nucleotide Motifs / genetics
  • Oligoribonucleotides / chemistry
  • Oligoribonucleotides / genetics
  • Oligoribonucleotides / metabolism
  • Protein Binding
  • Protein Structure, Tertiary*
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism
  • Sequence Homology, Nucleic Acid


  • LIN-28 protein, human
  • MicroRNAs
  • Oligoribonucleotides
  • RNA-Binding Proteins
  • mirnlet7 microRNA, human

Associated data

  • PDB/2LI8