Solution structure of domain I of the negative polarity CChMVd hammerhead ribozyme
Structure-function analysis of the ribozymes of chrysanthemum chlorotic mottle viroid: a loop-loop interaction motif conserved in most natural hammerheads
RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3')
Structures with the least restraint violations and total energy
minimized average structure of 29 converged conformers with the least restraint violation energy and total energy
simulated annealing and restrained energy minimization
0.5mM RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA, 100% D2O
0.5mM RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA, 90% H2O/10% D2O
1mM [U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA, 90% H2O/10% D2O
0.5mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA, 100% D2O
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo and Kollm
hammerhead ribozyme, viroid, CCHMVD, heptaloop, RNA