title: Improved Accuracy from Joint X-ray and NMR Refinement of a Protein-RNA Complex Structure.
abstract: Integrated experimental approaches play an increasingly important role in structural biology, taking advantage of the complementary information provided by different techniques. In particular, the combination of NMR data with X-ray diffraction patterns may provide accurate and precise information about local conformations not available from average-resolution X-ray structures alone. Here, we refined the structure of a ternary protein-protein-RNA complex comprising three domains, Sxl and Unr, bound to a single-stranded region derived in the msl2 mRNA. The joint X-ray and NMR refinement reveals that-despite the poor quality of the fit found for the original structural model-the NMR data can be largely accommodated within the uncertainty in the atom positioning (structural noise) from the primary X-ray data and that the overall domain arrangements and binding interfaces are preserved on passing from the crystalline state to the solution. The refinement highlights local conformational differences, which provide additional information on specific features of the structure. For example, conformational dynamics and heterogeneity observed at the interface between the CSD1 and the Sxl protein components in the ternary complex are revealed by the combination of NMR and crystallographic data. The joint refinement protocol offers unique opportunities to detect structural differences arising from various experimental conditions and reveals static or dynamic differences in the conformation of the biomolecule between the solution and the crystals.
authors.affiliation: Magnetic Resonance Center "CERM" and Department of Chemistry "Ugo Schiff", University of Florence and Magnetic Resonance Consortium (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino, Firenze, Italy.
authors.forename: Azzurra
authors.initials: A
authors.lastname: Carlon
authors.affiliation: Magnetic Resonance Center "CERM" and Department of Chemistry "Ugo Schiff", University of Florence and Magnetic Resonance Consortium (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino, Firenze, Italy.
authors.forename: Enrico
authors.initials: E
authors.lastname: Ravera
authors.affiliation: Center for Integrated Protein Science Munich (CIPSM) at Department Chemie, Technische Universität München , 85747 Garching, Germany.|Institute of Structural Biology, Helmholtz Zentrum München , 85764 Neuherberg, Germany.
authors.forename: Janosch
authors.initials: J
authors.lastname: Hennig
authors.affiliation: Magnetic Resonance Center "CERM" and Department of Chemistry "Ugo Schiff", University of Florence and Magnetic Resonance Consortium (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino, Firenze, Italy.
authors.forename: Giacomo
authors.initials: G
authors.lastname: Parigi
authors.affiliation: Center for Integrated Protein Science Munich (CIPSM) at Department Chemie, Technische Universität München , 85747 Garching, Germany.|Institute of Structural Biology, Helmholtz Zentrum München , 85764 Neuherberg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Sattler
authors.affiliation: Magnetic Resonance Center "CERM" and Department of Chemistry "Ugo Schiff", University of Florence and Magnetic Resonance Consortium (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino, Firenze, Italy.
authors.forename: Claudio
authors.initials: C
authors.lastname: Luchinat
mesh_terms: D008968:Molecular Conformation; D019906:Nuclear Magnetic Resonance, Biomolecular; D012313:RNA / Q000737:chemistry*; D016601:RNA-Binding Proteins / Q000737:chemistry*; D014961:X-Ray Diffraction
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA