2JSV

Dipole tensor-based refinement for atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR spectroscopy

Summary for 2JSV

• Entry DOI: 10.2210/pdb2jsv/pdb
• Related: 2GI9
• Descriptor: Immunoglobulin G-binding protein G (1 entity in total)
• Functional Keywords: ssnmr, gb1, tensor refinement, cell wall, igg-binding protein, peptidoglycan-anchor, immune system
• Biological source: Streptococcus sp. 'group G'
• Cellular location: Secreted, cell wall; Peptidoglycan-anchor (Potential): P19909
• Total number of polymer chains: 1
• Total formula weight: 6228.81

Authors

Franks, W.,Wylie, B.J.,Frericks, H.L.,Nieuwkoop, A.J.,Mayrhofer, R.,Shah, G.J.,Graesser, D.T.,Rienstra, C.M. (deposition date: 2007-07-16, release date: 2008-04-15, Last modification date: 2024-05-29)

Primary citation

Franks, W.T.,Wylie, B.J.,Schmidt, H.L.,Nieuwkoop, A.J.,Mayrhofer, R.M.,Shah, G.J.,Graesser, D.T.,Rienstra, C.M.
Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR
Proc.Natl.Acad.Sci.Usa, 105:4621-4626, 2008

PubMed Abstract: Magic-angle spinning (MAS) solid-state NMR (SSNMR) techniques have emerged in recent years for solving complete structures of uniformly labeled proteins lacking macroscopic order. Strategies used thus far have relied primarily on semiquantitative distance restraints, analogous to the nuclear Overhauser effect (NOE) routinely used in solution NMR. Here, we present a complementary approach for using relative orientations of molecular fragments, determined from dipolar line shapes. Whereas SSNMR distance restraints typically have an uncertainty of approximately 1 A, the tensor-based experiments report on relative vector (pseudobond) angles with precision of a few degrees. By using 3D techniques of this type, vector angle (VEAN) restraints were determined for the majority of the 56-residue B1 immunoglobulin binding domain of protein G [protein GB1 (a total of 47 HN-HN, 49 HN-HC, and 12 HA-HB restraints)]. By using distance restraints alone in the structure calculations, the overall backbone root-mean-square deviation (bbRMSD) was 1.01 +/- 0.13 A (1.52 +/- 0.12 A for all heavy atoms), which improved to 0.49 +/- 0.05 A (1.19 +/- 0.07 A) on the addition of empirical chemical shift [torsion angle likelihood obtained from shift and sequence similarity (TALOS)] restraints. VEAN restraints further improved the ensemble to 0.31 +/- 0.06 A bbRMSD (1.06 +/- 0.07 A); relative to the structure with distances alone, most of the improvement remained (bbRMSD 0.64 +/- 0.09 A; 1.29 +/- 0.07 A) when TALOS restraints were removed before refinement. These results represent significant progress toward atomic-resolution protein structure determination by SSNMR, capabilities that can be applied to a large range of membrane proteins and fibrils, which are often not amenable to solution NMR or x-ray crystallography.

PubMed: 18344321
DOI: 10.1073/pnas.0712393105

Experimental method

SOLID-STATE NMR