5LR4

RNA duplex has central consecutive GA pairs flanked by G-U basepairs with a methyl group on the adenine N6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.270 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Control of box C/D snoRNP assembly by N(6)-methylation of adenine.

Huang, L.Ashraf, S.Wang, J.Lilley, D.M.

(2017) EMBO Rep 18: 1631-1645

  • DOI: https://doi.org/10.15252/embr.201743967
  • Primary Citation of Related Structures:  
    5LQO, 5LQT, 5LR3, 5LR4, 5LR5

  • PubMed Abstract: 

    N 6 -methyladenine is the most widespread mRNA modification. A subset of human box C/D snoRNA species have target GAC sequences that lead to formation of N 6 -methyladenine at a key trans Hoogsteen-sugar A·G base pair, of which half are methylated in vivo The GAC target is conserved only in those that are methylated. Methylation prevents binding of the 15.5-kDa protein and the induced folding of the RNA Thus, the assembly of the box C/D snoRNP could in principle be regulated by RNA methylation at its critical first stage. Crystallography reveals that N 6 -methylation of adenine prevents the formation of trans Hoogsteen-sugar A·G base pairs, explaining why the box C/D RNA cannot adopt its kinked conformation. More generally, our data indicate that sheared A·G base pairs (but not Watson-Crick base pairs) are more susceptible to disruption by N 6 mA methylation and are therefore possible regulatory sites. The human signal recognition particle RNA and many related Alu retrotransposon RNA species are also methylated at N6 of an adenine that forms a sheared base pair with guanine and mediates a key tertiary interaction.


  • Organizational Affiliation

    Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, UK.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*(CBV)P*CP*GP*GP*(6MZ)P*UP*GP*GP*C)-3')
A, B, C, D
10Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.270 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.87α = 90
b = 49.87β = 90
c = 123.735γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Database references
  • Version 2.0: 2019-02-20
    Changes: Data collection, Polymer sequence
  • Version 2.1: 2019-07-10
    Changes: Data collection