2JSE
NMR reveals absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA.
Summary for 2JSE
| Entry DOI | 10.2210/pdb2jse/pdb |
| Descriptor | RNA (5'-R(*GP*GP*AP*GP*UP*GP*GP*CP*CP*GP*AP*AP*AP*GP*GP*CP*AP*UP*CP*UP*CP*C)-3') (1 entity in total) |
| Functional Keywords | nmr structure of rna loop 5' gugg 3' / 3' cuac 5', g base flipped out, 2x2 thermodynamics, lack of hydrogen bonding, absence of hydrogen bonding, uu internal loop, uu/ag internal loop, ag internal loop, internal loop from protein l11 binding site, rna |
| Total number of polymer chains | 1 |
| Total formula weight | 7112.31 |
| Authors | Shankar, N. (deposition date: 2007-07-03, release date: 2007-11-20, Last modification date: 2024-05-29) |
| Primary citation | Shankar, N.,Xia, T.,Kennedy, S.D.,Krugh, T.R.,Mathews, D.H.,Turner, D.H. NMR Reveals the Absence of Hydrogen Bonding in Adjacent UU and AG Mismatches in an Isolated Internal Loop from Ribosomal RNA Biochemistry, 46:12665-12678, 2007 Cited by PubMed Abstract: NMR studies provide insights into structural features of internal loops. These insights can be combined with thermodynamic studies to generate models for predicting structure and energetics. The tandem mismatch internal loop, 5'GUGG3'(3'CUAC5'), has been studied by NMR. The NMR structure reveals an internal loop with no hydrogen bonding between the loop bases and with the G in the AG mismatch flipped out of the helix. The sequence of this internal loop is highly conserved in rRNA. The loop is located in the large ribosomal subunit and is part of a conserved 58-nt fragment that is the binding domain of ribosomal protein L11. Structural comparisons between variants of this internal loop in crystal structures of the 58-nt domain complexed with L11 protein and of the large ribosomal subunit (LSU) suggest that this thermodynamically destabilizing internal loop is partially preorganized for tertiary interactions and for binding L11. A model for predicting the base pairing and free energy of 2 x 2 nucleotide internal loops with a purine-purine mismatch next to a pyrimidine-pyrimidine mismatch is proposed on the basis of the present NMR structure and previously reported thermodynamics. PubMed: 17929882DOI: 10.1021/bi700802s PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
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