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Single particle cryoEM has emerged as a powerful method for structure determination of proteins and complexes, complementing X-ray crystallography and NMR spectroscopy. Yet, for many systems, the resolution of cryoEM density map has been limited to 4-6 Å, which only allows for resolving bulky amino acids side chains, thus hindering accurate model building from the density map. On the other hand, experimental chemical shifts (CS) from solution and solid state MAS NMR spectra provide atomic level data for each amino acid within a molecule or a complex; however, structure determination of large complexes and assemblies based on NMR data alone remains challenging. Here, we present a novel integrated strategy to combine the highly complementary experimental data from cryoEM and NMR computationally by molecular dynamics simulations to derive an atomistic model, which is not attainable by either approach alone. We use the HIV-1 capsid protein (CA) C-terminal domain as well as the large capsid assembly to demonstrate the feasibility of this approach, termed NMR CS-biased cryoEM structure refinement.

Original publication

DOI

10.1021/acs.jpcb.6b13105

Type

Journal article

Journal

J Phys Chem B

Publication Date

20/04/2017

Volume

121

Pages

3853 - 3863

Keywords

Capsid Proteins, Cryoelectron Microscopy, Crystallography, X-Ray, HIV-1, Molecular Dynamics Simulation, Nuclear Magnetic Resonance, Biomolecular