The solution structure of the Lin28-ZnF domains bound to AGGAGAU of pre-let-7 miRNA

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: lowest energy/fewest violation 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


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

Loughlin, F.E.Gebert, L.F.Towbin, H.Brunschweiger, A.Hall, J.Allain, F.H.

(2011) Nat Struct Mol Biol 19: 84-89

  • DOI: https://doi.org/10.1038/nsmb.2202
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    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.

  • Organizational Affiliation

    Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein lin-28 homolog A74Homo sapiensMutation(s): 0 
Gene Names: CSDD1Lin-28aLIN28LIN28AZCCHC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9Z2 (Homo sapiens)
Explore Q9H9Z2 
Go to UniProtKB:  Q9H9Z2
GTEx:  ENSG00000131914 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H9Z2
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*AP*GP*GP*AP*GP*AP*U)-3')7N/A
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: lowest energy/fewest violation 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2012-01-25
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Derived calculations