2LI8 | pdb_00002li8

The solution structure of the Lin28-ZnF domains bound to AGGAGAU of pre-let-7 miRNA

• PDB DOI: https://doi.org/10.2210/pdb2LI8/pdb
• BMRB: 17883
• NAKB: 2LI8

• Classification: TRANSCRIPTION/RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-08-25 Released: 2011-12-07 
• Deposition Author(s): Allain, F.H.-T., Loughlin, F.E.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: lowest energy/fewest violation 

Literature

Structural basis of pre-let-7 miRNA recognition by the zinc knuckles of pluripotency factor Lin28.

Loughlin, F.E., Gebert, L.F., Towbin, H., Brunschweiger, A., Hall, J., Allain, F.H.

(2011) Nat Struct Mol Biol 19: 84-89

• PubMed: 22157959 
• DOI: https://doi.org/10.1038/nsmb.2202
• Primary Citation Related Structures: 
  2LI8


• PubMed Abstract: 
  

  Lin28 inhibits the biogenesis of let-7 miRNAs through a direct interaction with the terminal loop of pre-let-7. This interaction requires the zinc-knuckle domains of Lin28. We show that the zinc knuckle domains of Lin28 are sufficient to provide binding selectivity for pre-let-7 miRNAs and present the NMR structure of human Lin28 zinc knuckles bound to the short sequence 5'-AGGAGAU-3'. The structure reveals that each zinc knuckle recognizes an AG dinucleotide separated by a single nucleotide spacer. This defines a new 5'-NGNNG-3' consensus motif that explains how Lin28 selectively recognizes pre-let-7 family members. Binding assays in cell lysates and functional assays in cultured cells demonstrate that the interactions observed in the solution structure also occur between the full-length protein and members of the pre-let-7 family. The consensus sequence explains several seemingly disparate previously published observations on the binding properties of Lin28.

---

Organizational Affiliation: 
• Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 10.45 kDa 
• Atom Count: 632 
• Modeled Residue Count: 70 
• Deposited Residue Count: 81 
• 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	74	Homo sapiens	Mutation(s): 0  Gene Names: CSDD1, Lin-28a, LIN28, LIN28A, ZCCHC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9Z2 (Homo sapiens) Explore Q9H9Z2  Go to UniProtKB:  Q9H9Z2
PHAROS:  Q9H9Z2 GTEx:  ENSG00000131914

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*GP*GP*AP*GP*AP*U)-3')	B	7	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: lowest energy/fewest violation 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-07 
Deposition Author(s): Allain, F.H.-T., Loughlin, F.E.

Revision History  

• Version 1.0: 2011-12-07
  Type: Initial release
  
• Version 1.1: 2012-01-25
  Changes: Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Derived calculations