Mouse Lin28A in complex with let-7d microRNA pre-element

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Molecular Basis for Interaction of let-7 MicroRNAs with Lin28.

Nam, Y.Chen, C.Gregory, R.I.Chou, J.J.Sliz, P.

(2011) Cell 147: 1080-1091

  • DOI: https://doi.org/10.1016/j.cell.2011.10.020
  • Primary Citation of Related Structures:  
    3TRZ, 3TS0, 3TS2

  • PubMed Abstract: 

    MicroRNAs (miRNAs) are small noncoding RNA molecules that regulate gene expression. Among these, members of the let-7 miRNA family control many cell-fate determination genes to influence pluripotency, differentiation, and transformation. Lin28 is a specific, posttranscriptional inhibitor of let-7 biogenesis. We report crystal structures of mouse Lin28 in complex with sequences from let-7d, let-7-f1, and let-7 g precursors. The two folded domains of Lin28 recognize two distinct regions of the RNA and are sufficient for inhibition of let-7 in vivo. We also show by NMR spectroscopy that the linker connecting the two folded domains is flexible, accommodating Lin28 binding to diverse let-7 family members. Protein-RNA complex formation imposes specific conformations on both components that could affect downstream recognition by other processing factors. Our data provide a molecular explanation for Lin28 specificity and a model for how it regulates let-7.

  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein lin-28 homolog A
A, B, C, D, E
A, B, C, D, E, F
148Mus musculusMutation(s): 0 
Gene Names: Lin28aLin28Tex17
Find proteins for Q8K3Y3 (Mus musculus)
Explore Q8K3Y3 
Go to UniProtKB:  Q8K3Y3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8K3Y3
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*GP*GP*CP*AP*GP*GP*GP*AP*UP*UP*UP*UP*GP*CP*CP*CP*GP*GP*AP*G)-3')21synthetic construct
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
M [auth A]
N [auth A]
O [auth B]
P [auth B]
Q [auth C]
M [auth A],
N [auth A],
O [auth B],
P [auth B],
Q [auth C],
R [auth C],
S [auth D],
T [auth D],
U [auth E],
V [auth E],
W [auth F],
X [auth F]
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.82α = 90
b = 143.82β = 90
c = 177.72γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-16
    Type: Initial release
  • Version 1.1: 2011-11-30
    Changes: Database references
  • Version 1.2: 2011-12-14
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary