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PDBsum entry 1p79

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dna_rna metals links
RNA PDB id
1p79
Jmol
Contents
DNA/RNA
Metals
__K ×3
Waters ×90
PDB id:
1p79
Name: RNA
Title: Crystal structure of a bulged RNA tetraplex: implications for a novel binding site in RNA tetraplex
Structure: 5'-r( Up Gp Up Gp Gp U)-3'. Chain: a. Engineered: yes
Source: Synthetic: yes
Resolution:
1.10Å     R-factor:   0.127     R-free:   0.136
Authors: B.Pan,Y.Xiong,K.Shi,M.Sundaralingam
Key ref:
B.Pan et al. (2003). Crystal structure of a bulged RNA tetraplex at 1.1 a resolution: implications for a novel binding site in RNA tetraplex. Structure, 11, 1423-1430. PubMed id: 14604532 DOI: 10.1016/j.str.2003.09.017
Date:
30-Apr-03     Release date:   04-Nov-03    
 Headers
 References

 

 
DOI no: 10.1016/j.str.2003.09.017 Structure 11:1423-1430 (2003)
PubMed id: 14604532  
 
 
Crystal structure of a bulged RNA tetraplex at 1.1 a resolution: implications for a novel binding site in RNA tetraplex.
B.Pan, Y.Xiong, K.Shi, M.Sundaralingam.
 
  ABSTRACT  
 
Bulges are an important structural motif in RNA and can be used as recognition and interaction sites in RNA-protein interaction and RNA-RNA interaction. Here we report the first crystal structure of a bulged RNA tetraplex at 1.1 A resolution. The hexamer r(U)(BrdG)r(UGGU) forms a parallel tetraplex with the uridine sandwiched by guanines bulging out. The bulged uridine adopts the syn glycosidic conformation and its O2 and N3 atoms face outwards, serving as an effective recognition and interaction site. The bulge formation both widens the groove width and changes the groove hydrogen-bonding pattern on its 5' side. However, the bulge does not make any bends or kinks in the tetraplex structure. The present study demonstrates the dramatic difference between uridine and guanine in forming tetraplex structure. In addition, both G(syn) tetrad and G(anti) tetrad have been observed. They display the same base-pairing pattern and similar C1'-C1' distance but different hydrogen-bonding patterns in the groove.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Base Pairings in the Present Structure(A) BrdG(syn) tetrad; K+ ion is shown as big spheres and water molecules as small spheres. Hydrogen bonds are shown in dotted lines. (B) G(anti) tetrad; (C) U tetrad.
 
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 1423-1430) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20413582 G.W.Collie, S.M.Haider, S.Neidle, and G.N.Parkinson (2010).
A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex.
  Nucleic Acids Res, 38, 5569-5580.
PDB code: 3ibk
19823751 J.M.Lipay, and M.R.Mihailescu (2009).
NMR spectroscopy and kinetic studies of the quadruplex forming RNA r(UGGAGGU).
  Mol Biosyst, 5, 1347-1355.  
18832370 J.L.Huppert, A.Bugaut, S.Kumari, and S.Balasubramanian (2008).
G-quadruplexes: the beginning and end of UTRs.
  Nucleic Acids Res, 36, 6260-6268.  
18991403 S.Kumari, A.Bugaut, and S.Balasubramanian (2008).
Position and stability are determining factors for translation repression by an RNA G-quadruplex-forming sequence within the 5' UTR of the NRAS proto-oncogene.
  Biochemistry, 47, 12664-12669.  
17452368 J.Gros, F.Rosu, S.Amrane, A.De Cian, V.Gabelica, L.Lacroix, and J.L.Mergny (2007).
Guanines are a quartet's best friend: impact of base substitutions on the kinetics and stability of tetramolecular quadruplexes.
  Nucleic Acids Res, 35, 3064-3075.  
16381830 L.R.Stefan, R.Zhang, A.G.Levitan, D.K.Hendrix, S.E.Brenner, and S.R.Holbrook (2006).
MeRNA: a database of metal ion binding sites in RNA structures.
  Nucleic Acids Res, 34, D131-D134.  
16871639 M.Wieland, and J.S.Hartig (2006).
Turning inhibitors into activators: a hammerhead ribozyme controlled by a guanine quadruplex.
  Angew Chem Int Ed Engl, 45, 5875-5878.  
15914667 J.L.Huppert, and S.Balasubramanian (2005).
Prevalence of quadruplexes in the human genome.
  Nucleic Acids Res, 33, 2908-2916.  
15648098 M.Meyer, A.Hocquet, and J.Sühnel (2005).
Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads.
  J Comput Chem, 26, 352-364.  
  15562298 B.Pan, K.Shi, and M.Sundaralingam (2004).
Synthesis, Purification and Crystallization of Guanine-rich RNA Oligonucleotides.
  Biol Proced Online, 6, 257-262.  
14604520 J.A.Berglund (2003).
Expanding the structural repertoire of g-quadruplexes.
  Structure, 11, 1315-1316.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.