1YNG

NMR structure of the apoB mRNA stem-loop and its interaction with the C to U editing APOBEC1 complementary factor


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 16 
  • Selection Criteria: back calculated data agree with experimental NOESY spectrum,structures with the least restraint violations,structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

NMR structure of the apoB mRNA stem-loop and its interaction with the C to U editing APOBEC1 complementary factor.

Maris, C.Masse, J.Chester, A.Navaratnam, N.Allain, F.H.

(2005) RNA 11: 173-186

  • DOI: 10.1261/rna.7190705
  • Primary Citation of Related Structures:  
    1YLG, 1YNC, 1YNE, 1YNG

  • PubMed Abstract: 
  • We have solved the NMR structure of the 31-nucleotide (nt) apoB mRNA stem-loop, a substrate of the cytidine deaminase APOBEC1. We found that the edited base located at the 5' end of the octa-loop is stacked between two adenosines in both the unedited (cytidine 6666) and the edited (uridine 6666) forms and that the rest of the loop is unstructured ...

    We have solved the NMR structure of the 31-nucleotide (nt) apoB mRNA stem-loop, a substrate of the cytidine deaminase APOBEC1. We found that the edited base located at the 5' end of the octa-loop is stacked between two adenosines in both the unedited (cytidine 6666) and the edited (uridine 6666) forms and that the rest of the loop is unstructured. The 11-nt "mooring" sequence essential for editing is partially flexible although it is mostly in the stem of the RNA. The octa-loop and the internal loop in the middle of the stem confer this flexibility. These findings shed light on why APOBEC1 alone cannot edit efficiently the cytidine 6666 under physiological conditions, the editing base being buried in the loop and not directly accessible. We also show that APOBEC1 does not specifically bind apoB mRNA and requires the auxiliary factor, APOBEC1 complementary factor (ACF), to edit specifically cytidine 6666. The binding of ACF to both the mooring sequence and APOBEC1 explains the specificity of the reaction. Our NMR study lead us to propose a mechanism in which ACF recognizes first the flexible nucleotides of the mooring sequence (the internal loop and the 3' end octa-loop) and subsequently melts the stem-loop, exposing the amino group of the cytidine 6666 to APOBEC1. Thus, the flexibility of the mooring sequence plays a central role in the RNA recognition by ACF.


    Organizational Affiliation

    Institute for Molecular Biology and Biophysics, ETH Hönggerberg HPK D11.2, CH-8093 Zürich, Switzerland.



Macromolecules
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Entity ID: 1
MoleculeChainsLengthOrganismImage
apolipoprotein B mRNAA 31N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 16 
  • Selection Criteria: back calculated data agree with experimental NOESY spectrum,structures with the least restraint violations,structures with the lowest energy 
  • OLDERADO: 1YNG Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-08
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Data collection, Database references, Derived calculations