5UDZ

Human LIN28A in complex with let-7f-1 microRNA pre-element


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

LIN28 Zinc Knuckle Domain Is Required and Sufficient to Induce let-7 Oligouridylation.

Wang, L.Nam, Y.Lee, A.K.Yu, C.Roth, K.Chen, C.Ransey, E.M.Sliz, P.

(2017) Cell Rep 18: 2664-2675

  • DOI: 10.1016/j.celrep.2017.02.044

  • PubMed Abstract: 
  • LIN28 is an RNA binding protein that plays crucial roles in pluripotency, glucose metabolism, tissue regeneration, and tumorigenesis. LIN28 binds to the let-7 primary and precursor microRNAs through bipartite recognition and induces degradation of le ...

    LIN28 is an RNA binding protein that plays crucial roles in pluripotency, glucose metabolism, tissue regeneration, and tumorigenesis. LIN28 binds to the let-7 primary and precursor microRNAs through bipartite recognition and induces degradation of let-7 precursors (pre-let-7) by promoting oligouridylation by terminal uridylyltransferases (TUTases). Here, we report that the zinc knuckle domain (ZKD) of mouse LIN28 recruits TUT4 to initiate the oligouridylation of let-7 precursors. Our crystal structure of human LIN28 in complex with a fragment of pre-let-7f-1 determined to 2.0 Å resolution shows that the interaction between ZKD and RNA is constrained to a small cavity with a high druggability score. We demonstrate that the specific interaction between ZKD and pre-let-7 is necessary and sufficient to induce oligouridylation by recruiting the N-terminal fragment of TUT4 (NTUT4) and the formation of a stable ZKD:NTUT4:pre-let-7 ternary complex is crucial for the acquired processivity of TUT4.


    Related Citations: 
    • 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


    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
148Homo sapiensGene Names: LIN28A (CSDD1, LIN28, ZCCHC1)
Find proteins for Q9H9Z2 (Homo sapiens)
Go to Gene View: LIN28A
Go to UniProtKB:  Q9H9Z2
Entity ID: 2
MoleculeChainsLengthOrganism
let-7f-1 pre-elementV,W25Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.164 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 76.429α = 90.00
b = 76.429β = 90.00
c = 105.615γ = 90.00
Software Package:
Software NamePurpose
AutoPROCdata scaling
XDSdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesR01CA163647

Revision History 

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-03-29
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence