3ULJ

Crystal structure of apo Lin28B cold shock domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.121 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 7492-7506

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

  • 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- ...

    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
Lin28b, DNA-binding proteinA, B90Xenopus tropicalisMutation(s): 0 
Gene Names: lin28b, oscp1
Find proteins for B4F6I0 (Xenopus tropicalis)
Explore B4F6I0 
Go to UniProtKB:  B4F6I0
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.121 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.62α = 90
b = 52.62β = 90
c = 137.336γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2012-10-24
    Changes: Database references