Cryo-EM structure of the native rhodopsin dimer in nanodiscs

J Biol Chem. 2019 Sep 27;294(39):14215-14230. doi: 10.1074/jbc.RA119.010089. Epub 2019 Aug 9.


Imaging of rod photoreceptor outer-segment disc membranes by atomic force microscopy and cryo-electron tomography has revealed that the visual pigment rhodopsin, a prototypical class A G protein-coupled receptor (GPCR), can organize as rows of dimers. GPCR dimerization and oligomerization offer possibilities for allosteric regulation of GPCR activity, but the detailed structures and mechanism remain elusive. In this investigation, we made use of the high rhodopsin density in the native disc membranes and of a bifunctional cross-linker that preserves the native rhodopsin arrangement by covalently tethering rhodopsins via Lys residue side chains. We purified cross-linked rhodopsin dimers and reconstituted them into nanodiscs for cryo-EM analysis. We present cryo-EM structures of the cross-linked rhodopsin dimer as well as a rhodopsin dimer reconstituted into nanodiscs from purified monomers. We demonstrate the presence of a preferential 2-fold symmetrical dimerization interface mediated by transmembrane helix 1 and the cytoplasmic helix 8 of rhodopsin. We confirmed this dimer interface by double electron-electron resonance measurements of spin-labeled rhodopsin. We propose that this interface and the arrangement of two protomers is a prerequisite for the formation of the observed rows of dimers. We anticipate that the approach outlined here could be extended to other GPCRs or membrane receptors to better understand specific receptor dimerization mechanisms.

Keywords: G protein-coupled receptor (GPCR); cell signaling; cryo-electron microscopy (cryo-EM); double electron-electron resonance (DEER); helix 8 (H8); receptor; retina; retinoid-binding protein; rhodopsin; rhodopsin dimerization; rod outer segment; transducin; transmembrane helix 1 (TM1).

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cattle
  • Cryoelectron Microscopy
  • HEK293 Cells
  • Humans
  • Nanoparticles / chemistry*
  • Protein Domains
  • Protein Multimerization*
  • Rhodopsin / chemistry*
  • Rhodopsin / ultrastructure


  • Rhodopsin

Associated data

  • PDB/1U19
  • PDB/3PXO
  • PDB/4GPO
  • PDB/6OFJ