9Y7F
Crystal structure of nanobody R3D8 in complex with human voltage-gated sodium channel Nav1.7 P-loop 1.
Summary for 9Y7F
| Entry DOI | 10.2210/pdb9y7f/pdb |
| Descriptor | Nanobody R3D8, Sodium channel protein type 9 subunit alpha (3 entities in total) |
| Functional Keywords | voltage-gated sodium channel, nav1.7, nanobody, membrane protein |
| Biological source | Vicugna pacos (alpaca) More |
| Total number of polymer chains | 2 |
| Total formula weight | 17883.65 |
| Authors | |
| Primary citation | Liu, J.,Chen, W.,Cristofori-Armstrong, B.,Crawford, T.,Chen, K.E.,Xie, P.,Chan, R.W.B.,Zhu, Y.,Golder, M.,Pereira Schmidt, A.,Naughton, J.D.,Condon, N.D.,Andersson, A.,Dehkhoda, F.,McMahon, K.L.,Klasfauseweh, T.,Thapa, A.,Tran, H.,Tran, P.,Jami, S.,Ragnarsson, L.,Furness, S.G.B.,Deuis, J.R.,Collins, B.M.,Tham, W.H.,Prasadam, I.,Vetter, I.,Mobli, M. Antigen-Detected NMR for Minimal Epitope Engineering and Structure-Guided Selection of a Na V 1.7-Selective Nanobody. Adv Sci, :e77611-e77611, 2026 Cited by PubMed Abstract: Selective molecular recognition of membrane proteins is challenging because they contain few solvent-exposed extracellular epitopes, which often depend on their native environment for structure, making them difficult to isolate faithfully for binder discovery. Here, we show that antigen-detected NMR is well suited both to characterizing the folding of engineered minimal epitopes from the human voltage-gated sodium channel Na1.7 and to selecting binders that recognize their solvent-exposed surfaces. Isotope labelling of the antigen enables NMR resonance assignment to assess retained local secondary structure, while N titration and zz-exchange mapping provide binding and interface information. Combined with AlphaFold2 complex prediction, this creates a practical method for screening and ranking candidate binders. The approach was further validated by a high-resolution x-ray structure of an antigen-nanobody complex. Applying this workflow identified R4C8, a subtype- and species-selective nanobody whose binding to the extracellular surface of human Na1.7 is supported by zz-exchange mapping, modelling, and cellular recognition, and which has minimal effects on channel gating. R4C8 detected Na1.7 in engineered cell lines and in primary osteoarthritis-derived chondrocytes, providing a useful tool for selective target detection. These results show how antigen-detected NMR can support peptide engineering and structure-guided protein binder selection against minimal epitopes. PubMed: 42702812DOI: 10.1002/advs.77611 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.7 Å) |
Structure validation
Download full validation report
