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TitleStructural analysis of rhodopsin states in megabody complexes.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 123, Issue 6, Page e2532336123, Year 2026
Publish dateFeb 10, 2026
AuthorsDavid Salom / Diana S Suder / Wei Huang / Arum Wu / Els Pardon / Jan Steyaert / Philip D Kiser / Derek J Taylor / Shane Gonen / Krzysztof Palczewski /
PubMed AbstractRhodopsin, 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 ...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.
External linksProc Natl Acad Sci U S A / PubMed:41650224 / PubMed Central
MethodsEM (single particle)
Resolution3.1 - 3.94 Å
Structure data

49589

9nnz

EMDB-49589: A membrane protein with cofactor determined by single-particle CryoEM
PDB-9nnz: Structure of rod opsin in complex with a megabody
Method: EM (single particle) / Resolution: 3.94 Å

49622

9noz

EMDB-49622, PDB-9noz:
Structure of photoactivated rhodopsin in complex with a megabody
Method: EM (single particle) / Resolution: 3.48 Å

49945

9nyx

EMDB-49945, PDB-9nyx:
Structure of Native Bovine Rhodopsin in Complex with Mb7 in the Dark State
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

ChemComp-RET:
RETINAL

Source
  • bos taurus (domestic cattle)
  • synthetic construct (others)
  • lama glama (llama)
KeywordsMEMBRANE PROTEIN / opsin / megabody / nanobody / rhodopsin / ISOMERASE/IMMUNE SYSTEM / nanoboy / native purification / dark state / retinal / ISOMERASE-IMMUNE SYSTEM complex

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