GSNVFNNTITHPNAGPTSATSTSTSSNGNTPLSSNSSMNPKSLTDPKLLKNIPMWLKSLRLHKYSDALSGTPWIELIYLD DETLEKKGVLALGARRKLLKAFGIVIDYKERDLIDRSAY
crystal structure of the unliganded Vts1 SAM domain
RNA was produced by T7 polymerase based in vitro transcription
Protein NOE restraints were calibrated from peak volumes to distances ranging from 1.8-5.0 using the CANDID module of CYANA v2.1. Initially, 100 structures were calculated with XPLOR-NIH v2.11.0 starting from a partially docked protein-RNA complex. A simulated annealing approach with internal torsion angle dynamics, delphic database potentials and RNA planarity restraints was used. From the initial ensemble of structures, 20 were selected based upon low energy, no NOE violations > 0.5 angstroms and no dihedral angle violations > 5 degrees. Restraints used for the structure calculation: 882 intraresidue protein-protein NOE, 435 sequential protein-protein NOE, 335 medium range protein-protein NOE, 263 long range protein-protein NOE, 80 protein hydrogen bonds, 60 RNA-RNA NOE, 23 protein-RNA NOE, 140 protein dihedral angle, 93 RNA dihedral angle.
0.2-0.8 mM U-15N,13C; 20 mM sodium phosphate buffer, pH 7.8, 150 mM sodium chloride, 0.02 % sodium azide
alpha-helix, pentaloop, hairpin, RNA BINDING PROTEIN
NVFNNTITHPNAGPTSATSTSTSSNGNTPLSSNSSMNPKSLTDPKLLKNIPMWLKSLRLHKYSDALSGTPWIELIYLDDE TLEKKGVLALGARRKLLKAFGIVIDYKERDLIDRSAY