Joint X-ray/NMR structure refinement of multidomain/multisubunit systems

  • Azzurra Carlon
  • Enrico Ravera
  • Giacomo Parigi
  • Garib N. Murshudov
  • Claudio LuchinatEmail author


Data integration in structural biology has become a paradigm for the characterization of biomolecular systems, and it is now accepted that combining different techniques can fill the gaps in each other’s blind spots. In this frame, one of the combinations, which we have implemented in REFMAC-NMR, is residual dipolar couplings from NMR together with experimental data from X-ray diffraction. The first are exquisitely sensitive to the local details but does not give any information about overall shape, whereas the latter encodes more the information about the overall shape but at the same time tends to miss the local details even at the highest resolutions. Once crystals are obtained, it is often rather easy to obtain a complete X-ray dataset, however it is time-consuming to obtain an exhaustive NMR dataset. Here, we discuss the effect of including a-priori knowledge on the properties of the system to reduce the number of experimental data needed to obtain a more complete picture. We thus introduce a set of new features of REFMAC-NMR that allow for improved handling of RDC data for multidomain proteins and multisubunit biomolecular complexes, and encompasses the use of pseudo-contact shifts as an additional source of NMR-based information. The new feature may either help in improving the refinement, or assist in spotting differences between the crystal and the solution data. We show three different examples where NMR and X-ray data can be reconciled to a unique structural model without invoking mobility.


Structure refinement Residual dipolar couplings Integrated structural biology REFMAC 



The support from Fondazione Cassa di Risparmio di Firenze, MIUR PRIN 2012SK7ASN, the European Commission projects iNEXT No. 653706, West-Life No. 675858, EMBO ASTF 620–2015, and Instruct-ERIC, a Landmark ESFRI project, and specifically the CERM/CIRMMP Italy center, is acknowledged. GNM is funded by Medical Research Council (Grant No. MC_UP_A025_1012). Extensive and frank discussions with Christian Griesinger on how much information on dynamics can be reliably extracted from the NMR data of CaM-IQ are acknowledged.

Supplementary material

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Supplementary material 1 (DOCX 3299 KB)


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© Springer Nature B.V. 2018

Authors and Affiliations

  1. 1.Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP)Sesto FiorentinoItaly
  2. 2.Department of Chemistry “Ugo Schiff”University of FlorenceSesto FiorentinoItaly
  3. 3.MRC Laboratory for Molecular BiologyCambridgeUK

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