4A76

The Lin28b Cold shock domain in complex with heptathymidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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: https://doi.org/10.1093/nar/gks355
  • Primary Citation of Related Structures:  
    3ULJ, 4A4I, 4A75, 4A76, 4ALP

  • 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-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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LIN28 COLD SHOCK DOMAIN
A, C, E, G
90Xenopus tropicalisMutation(s): 0 
UniProt
Find proteins for B4F6I0 (Xenopus tropicalis)
Explore B4F6I0 
Go to UniProtKB:  B4F6I0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4F6I0
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*TP*TP*TP*TP*TP*TP*TP)-3'
B, D, F, H
7N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.61α = 90
b = 77.575β = 90
c = 100.231γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Data collection
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Other