3TS0 | pdb_00003ts0

Mouse Lin28A in complex with let-7f-1 microRNA pre-element

• PDB DOI: https://doi.org/10.2210/pdb3TS0/pdb
• NAKB: 3TS0

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 
  0.214 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

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

• PubMed: 22078496 
• DOI: https://doi.org/10.1016/j.cell.2011.10.020
• Primary Citation 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.83 kDa 
• Atom Count: 3,068 
• Modeled Residue Count: 318 
• Deposited Residue Count: 338 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein lin-28 homolog A	A, B	146	Mus musculus	Mutation(s): 0  Gene Names: Lin28, Lin28a, Tex17
UniProt
Find proteins for Q8K3Y3 (Mus musculus) Explore Q8K3Y3  Go to UniProtKB:  Q8K3Y3

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*GP*GP*UP*AP*GP*UP*GP*AP*UP*UP*UP*UP*AP*CP*CP*CP*UP*GP*GP*AP*G)-3')	C [auth U], D [auth V]	23	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free:  0.214 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/2

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.88	α = 90
b = 139.88	β = 90
c = 85.55	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
autoPROC	data scaling
SCALA	data scaling
PHASER	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2011-12-14
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description