9NYX
Structure of Native Bovine Rhodopsin in Complex with Mb7 in the Dark State
Summary for 9NYX
| Entry DOI | 10.2210/pdb9nyx/pdb |
| EMDB information | 49945 |
| Descriptor | Megabody 7, Rhodopsin, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (5 entities in total) |
| Functional Keywords | nanoboy, rhodopsin, native purification, dark state, retinal, isomerase-immune system complex, isomerase/immune system |
| Biological source | Lama glama (llama) More |
| Total number of polymer chains | 4 |
| Total formula weight | 101595.54 |
| Authors | Huang, W.,Salom-Arbona, D.,Suder, D.,Taylor, D.J.,Palczewski, K. (deposition date: 2025-03-29, release date: 2026-02-04, Last modification date: 2026-03-18) |
| Primary citation | Salom, D.,Suder, D.S.,Huang, W.,Wu, A.,Pardon, E.,Steyaert, J.,Kiser, P.D.,Taylor, D.J.,Gonen, S.,Palczewski, K. Structural analysis of rhodopsin states in megabody complexes. Proc.Natl.Acad.Sci.USA, 123:e2532336123-e2532336123, 2026 Cited by PubMed Abstract: Rhodopsin, the most intensively studied G protein-coupled receptor (GPCR), is activated by light-induced isomerization of its chromophore 11--retinal. This study employed cryogenic electron microscopy (cryo-EM) to investigate rhodopsin structure using a megabody (Mb7) as a negative allosteric modulator. Three distinct cryo-EM structures were solved: ground-state rhodopsin, photoactivated rhodopsin, and apo-rhodopsin, all in complex with Mb7. Photoactivated rhodopsin and apo-rhodopsin, both in complex with Mb7, maintain a conformation remarkably similar to ground-state rhodopsin rather than adopting a Meta-II-like conformation. Structural elements, including the conserved residues of the NPxxY motif and the ionic lock, remain in positions corresponding to inactive rhodopsin. The megabody forms extensive interactions with rhodopsin's extracellular loop 2, N terminus, and glycans. The findings demonstrate that Mb7 stabilizes photoactivated rhodopsin in a Meta-I-like conformation, preventing progression to the active Meta-II state through specific immobilization of the extracellular domain. This work establishes a foundation for cryo-EM-guided discovery of ligands modulating rhodopsin. PubMed: 41650224DOI: 10.1073/pnas.2532336123 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.1 Å) |
Structure validation
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