PDBsum entry 1mdg

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dna_rna ligands metals links
_NA ×5
Waters ×16
PDB id:
Name: RNA
Title: An alternating antiparallel octaplex in an RNA crystal struc
Structure: 5'-r( Up (Bgm)gp Ap Gp Gp U)-3'. Chain: a. Engineered: yes
Source: Synthetic: yes
Biol. unit: Octamer (from PDB file)
1.50Å     R-factor:   0.172     R-free:   0.194
Authors: B.C.Pan,Y.Xiong,K.Shi,M.Sundaralingam
Key ref:
B.Pan et al. (2003). An eight-stranded helical fragment in RNA crystal structure: implications for tetraplex interaction. Structure, 11, 825-831. PubMed id: 12842045 DOI: 10.1016/S0969-2126(03)00108-4
07-Aug-02     Release date:   12-Aug-03    


DOI no: 10.1016/S0969-2126(03)00108-4 Structure 11:825-831 (2003)
PubMed id: 12842045  
An eight-stranded helical fragment in RNA crystal structure: implications for tetraplex interaction.
B.Pan, Y.Xiong, K.Shi, M.Sundaralingam.
Multistranded helical structures in nucleic acids play various functions in biological processes. Here we report the crystal structure of a hexamer, rU(BrdG)r(AGGU),at 1.5 A resolution containing a structural complex of an alternating antiparallel eight-stranded helical fragment that is sandwiched in two tetraplexes. The octaplex is formed by groove binding interaction and base tetrad intercalation between two tetraplexes. Two different forms of octaplexes have been proposed, which display different properties in interaction with proteins and nucleic acids. Adenines form a base tetrad in the novel N6-H em leader N3 conformation and further interact with uridines to form an adenine-uridine octad in the reverse Hoogsteen pairing scheme. The conformational flexibility of adenine tetrad indicates that it can optimize its conformation in different interactions.
  Selected figure(s)  
Figure 3.
Figure 3. Hydration and Cobalt Hexammine Interaction(A) A stereo view of hydration of the deep grooves in the octaplex. Water molecules, green; cobalt hexammine ion, blue.(B) A stereoview of the hydration in the shallow groove in the octaplex.(C) A cobalt hexammine ion sits near the junctions of two tetraplexes and the deep groove of the octaplex, participating in lattice interactions.
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 825-831) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20882216 A.K.Mishra, R.K.Prajapati, and S.Verma (2010).
Probing structural consequences of N9-alkylation in silver-adenine frameworks.
  Dalton Trans, 39, 10034-10037.  
19943071 T.van der Wijst, B.Lippert, M.Swart, C.F.Guerra, and F.M.Bickelhaupt (2010).
Differential stabilization of adenine quartets by anions and cations.
  J Biol Inorg Chem, 15, 387-397.  
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.  
17913750 D.J.Patel, A.T.Phan, and V.Kuryavyi (2007).
Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics.
  Nucleic Acids Res, 35, 7429-7455.  
16086347 P.Amo-Ochoa, P.J.Sanz Miguel, P.Lax, I.Alonso, M.Roitzsch, F.Zamora, and B.Lippert (2005).
Models of putative (AH)G(AH)G nucleobase quartets.
  Angew Chem Int Ed Engl, 44, 5670-5674.  
  15562298 B.Pan, K.Shi, and M.Sundaralingam (2004).
Synthesis, Purification and Crystallization of Guanine-rich RNA Oligonucleotides.
  Biol Proced Online, 6, 257-262.  
14604532 B.Pan, Y.Xiong, K.Shi, and M.Sundaralingam (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.
PDB code: 1p79
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