3TRZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.cell.2011.10.020
  • Primary Citation of Related Structures:  3TS0, 3TS2
  • Also Cited By: 5UDZ

  • 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 s ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein lin-28 homolog A
A, B, C, D, E, F
148Mus musculusGene Names: Lin28a (Lin28, Tex17)
Find proteins for Q8K3Y3 (Mus musculus)
Go to UniProtKB:  Q8K3Y3
Entity ID: 2
MoleculeChainsLengthOrganism
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')U,V,W,X,Y,Z21N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GMP
Query on GMP
U, V, W, X, Y, Z
NON-POLYMERC10 H13 N5 O5

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 
  • Space Group: P 43 21 2
  • Diffraction Data DOI: 
    10.15785/SBGRID/3 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 143.820α = 90.00
b = 143.820β = 90.00
c = 177.720γ = 90.00
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
XDSdata reduction
ADSCdata collection
SCALAdata scaling
BUSTERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-09-11 
  • Released Date: 2011-11-16 
  • Deposition Author(s): Nam, Y., Sliz, P.

Revision History 

  • Version 1.0: 2011-11-16
    Type: Initial release
  • Version 1.1: 2011-11-30
    Type: Database references
  • Version 1.2: 2011-12-14
    Type: Database references