9B4V

4F-Trp labeled Oscillatoria Agardhii Agglutinin (OAA)

Summary for 9B4V

• Entry DOI: 10.2210/pdb9b4v/pdb
• NMR Information: BMRB: 31152
• Descriptor: Lectin (1 entity in total)
• Functional Keywords: beta barrel, carbohydrate binding, sugar binding protein
• Biological source: Oscillatoria agardhii
• Total number of polymer chains: 1
• Total formula weight: 14169.90

Authors

Runge, B.R.,Zadorozhnyi, R.R.,Quinn, C.M.,Russell, R.W.,Lu, M.,Antolinez, S.,Struppe, J.,Schwieters, C.D.,Byeon, I.L.,Hadden-Perilla, J.,Gronenborn, A.M.,Polenova, T. (deposition date: 2024-03-21, release date: 2024-11-06, Last modification date: 2024-11-20)

Primary citation

Runge, B.R.,Zadorozhnyi, R.,Quinn, C.M.,Russell, R.W.,Lu, M.,Antolinez, S.,Struppe, J.,Schwieters, C.D.,Byeon, I.L.,Hadden-Perilla, J.A.,Gronenborn, A.M.,Polenova, T.
Integrating 19 F Distance Restraints for Accurate Protein Structure Determination by Magic Angle Spinning NMR Spectroscopy.
J.Am.Chem.Soc., 146:30483-30494, 2024

PubMed Abstract: Traditional protein structure determination by magic angle spinning (MAS) solid-state NMR spectroscopy primarily relies on interatomic distances up to 8 Å, extracted from C-, N-, and H-based dipolar-based correlation experiments. Here, we show that F fast (60 kHz) MAS NMR spectroscopy can supply additional, longer distances. Using 4F-Trp,U-C,N crystalline agglutinin (OAA), we demonstrate that judiciously designed 2D and 3D F-based dipolar correlation experiments such as (H)CF, (H)CHF, and FF can yield interatomic distances in the 8-16 Å range. Incorporation of fluorine-based restraints into structure calculation improved the precision of Trp side chain conformations as well as regions in the protein around the fluorine containing residues, with notable improvements observed for residues in proximity to the Trp pairs (W10/W17 and W77/W84) in the carbohydrate-binding loops, which lacked sufficient long-range C-C distance restraints. Our work highlights the use of fluorine and F fast MAS NMR spectroscopy as a powerful structural biology tool.

PubMed: 39440810
DOI: 10.1021/jacs.4c11373

Experimental method

SOLID-STATE NMR