4A75

The Lin28b Cold shock domain in complex with hexathymidine.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Lin28 Cold-Shock Domain Remodels Pre-Let-7 Microrna.

Mayr, F.Schutz, A.Doge, N.Heinemann, U.

(2012) Nucleic Acids Res 40: 7492

  • DOI: 10.1093/nar/gks355
  • Primary Citation of Related Structures:  
    3ULJ, 4ALP, 4A4I, 4A75, 4A76

  • PubMed Abstract: 
  • The RNA-binding protein Lin28 regulates the processing of a developmentally important group of microRNAs, the let-7 family. Lin28 blocks the biogenesis of let-7 in embryonic stem cells and thereby prevents differentiation. It was shown that both RNA-bind ...

    The RNA-binding protein Lin28 regulates the processing of a developmentally important group of microRNAs, the let-7 family. Lin28 blocks the biogenesis of let-7 in embryonic stem cells and thereby prevents differentiation. It was shown that both RNA-binding domains (RBDs) of this protein, the cold-shock domain (CSD) and the zinc-knuckle domain (ZKD) are indispensable for pri- or pre-let-7 binding and blocking its maturation. Here, we systematically examined the nucleic acid-binding preferences of the Lin28 RBDs and determined the crystal structure of the Lin28 CSD in the absence and presence of nucleic acids. Both RNA-binding domains bind to single-stranded nucleic acids with the ZKD mediating specific binding to a conserved GGAG motif and the CSD showing only limited sequence specificity. However, only the isolated Lin28 CSD, but not the ZKD, can bind with a reasonable affinity to pre-let-7 and thus is able to remodel the terminal loop of pre-let-7 including the Dicer cleavage site. Further mutagenesis studies reveal that the Lin28 CSD induces a conformational change in the terminal loop of pre-let-7 and thereby facilitates a subsequent specific binding of the Lin28 ZKD to the conserved GGAG motif.


    Organizational Affiliation

    Crystallography, Max-Delbrück Center for Molecular Medicine, Robert-Rössle Straße 10, 13125 Berlin, Germany.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LIN28 COLD SHOCK DOMAIN ACEG90Xenopus tropicalisMutation(s): 0 
Gene Names: lin28b
Find proteins for B4F6I0 (Xenopus tropicalis)
Explore B4F6I0 
Go to UniProtKB:  B4F6I0
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*TP*TP*TP*TP*TP*TP)-3'B, D, F, H6synthetic construct
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SCN
    Query on SCN

    Download Ideal Coordinates CCD File 
    A, E
    THIOCYANATE ION
    C N S
    ZMZDMBWJUHKJPS-UHFFFAOYSA-M
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.75 Å
    • R-Value Free: 0.198 
    • R-Value Work: 0.171 
    • R-Value Observed: 0.172 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 51.799α = 90
    b = 81.822β = 90
    c = 99.819γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2012-09-05
      Type: Initial release
    • Version 1.1: 2018-04-04
      Changes: Data collection
    • Version 1.2: 2019-10-09
      Changes: Data collection, Experimental preparation, Other, Source and taxonomy