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: 1.8 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.269 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.15252/embr.201743967
  • Primary Citation of Related Structures:  5LQO, 5LQT, 5LR3, 5LR5

  • PubMed Abstract: 
  • N6-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 N6-methyladenine at a key trans Hoogsteen-sugar A·G base pair, of which half are methylated in viv ...

    N6-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 N6-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 N6-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 N6mA 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*(CBV)P*CP*GP*GP*(6MZ)P*UP*GP*GP*C)-3')A,B,C,D10Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
6MZ
Query on 6MZ
A, B, C, D
RNA LINKINGC11 H16 N5 O7 PA
CBV
Query on CBV
A, B, C, D
RNA LINKINGC9 H13 Br N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.269 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 49.870α = 90.00
b = 49.870β = 90.00
c = 123.735γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXphasing
PHENIXrefinement
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-06-28
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Database references