Atomic resolution protein structure determination by three-dimensional transferred echo double resonance solid-state nuclear magnetic resonance spectroscopy

We show that quantitative internuclear N-15-C-13 distances can be obtained in sufficient quantity to determine a complete, high-resolution structure of a moderately sized protein by magic-angle spinning solid-state NMR spectroscopy. The three-dimensional ZF-TEDOR pulse sequence is employed in combination with sparse labeling of C-13 sites in the beta 1 domain of the immunoglobulin binding protein G (GB1), as obtained by bacterial expression with 1,3-C-13 or 2-C-13-glycerol as the C-13 source. Quantitative dipolar trajectories are extracted from two-dimensional N-15-C-13 planes, in which similar to 750 cross peaks are resolved. The experimental data are fit to exact theoretical trajectories for spin clusters (consisting of one C-13 and several N-15 each), yielding quantitative precision as good as 0.1 A degrees for similar to 350 sites, better than 0.3 A degrees for another 150, and similar to 1.0 A degrees for 150 distances in the range of 5-8 A degrees. Along with isotropic chemical shift-based (TALOS) dihedral angle restraints, the distance restraints are incorporated into simulated annealing calculations to yield a highly precise structure (backbone RMSD of 0.25 +/- 0.09 A degrees), which also demonstrates excellent agreement with the most closely related crystal structure of GB1 (2QMT, bbRMSD 0.79 +/- 0.03 A degrees). Moreover, side chain heavy atoms are well restrained (0.76 +/- 0.06 A degrees total heavy atom RMSD). These results demonstrate for the first time that quantitative internuclear distances can be measured throughout an entire solid protein to yield an atomic-resolution structure.