1MDG

An Alternating Antiparallel Octaplex in an RNA Crystal Structure

Summary for 1MDG

• Entry DOI: 10.2210/pdb1mdg/pdb
• Descriptor: 5'-R(*UP*(BGM)GP*AP*GP*GP*U)-3', SODIUM ION, COBALT HEXAMMINE(III), ... (4 entities in total)
• Functional Keywords: tetraplex, base tetrads, base octads, rna
• Total number of polymer chains: 1
• Total formula weight: 2271.16

Authors

Pan, B.C.,Xiong, Y.,Shi, K.,Sundaralingam, M. (deposition date: 2002-08-07, release date: 2003-08-12, Last modification date: 2024-02-14)

Primary citation

Pan, B.C.,Xiong, Y.,Shi, K.,Sundaralingam, M.
An Eight-Stranded Helical Fragment in RNA Crystal Structure: Implications for Tetraplex Interaction
Structure, 11:825-831, 2003

PubMed Abstract: 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.

PubMed: 12842045
DOI: 10.1016/S0969-2126(03)00108-4

Experimental method

X-RAY DIFFRACTION (1.5 Å)