6OFJ

Cryo-EM structure of the native rhodopsin dimer from rod photoreceptor cells


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Cryo-EM structure of the native rhodopsin dimer in nanodiscs.

Zhao, D.Y.Poge, M.Morizumi, T.Gulati, S.Van Eps, N.Zhang, J.Miszta, P.Filipek, S.Mahamid, J.Plitzko, J.M.Baumeister, W.Ernst, O.P.Palczewski, K.

(2019) J.Biol.Chem. 294: 14215-14230

  • DOI: 10.1074/jbc.RA119.010089

  • PubMed Abstract: 
  • Imaging of rod photoreceptor outer-segment disc membranes by atomic force microscopy (AFM) 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 ...

    Imaging of rod photoreceptor outer-segment disc membranes by atomic force microscopy (AFM) 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 crosslinked rhodopsin dimer as well as a rhodopsin dimer reconstituted into nanodiscs from purified monomers. We demonstrate the presence of a preferential two-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 (DEER) 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.


    Organizational Affiliation

    Max Planck Institute of Biochemistry, Germany.,Gavin Herbert Eye Institute, University of California, Irvine, United States.,Molecular Structural Biology, Max Planck Institute of Biochemistry, Germany.,Max Planck Institute of Biochemistry.,University of Toronto, Canada.,Biological and Chemical Research Centre; University of Warsaw, Poland.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Germany.,Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Poland.,Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, United States.,Biochemistry, University of Toronto, Canada.,Case Western Reserve University.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rhodopsin
A, B
348Bos taurusMutation(s): 0 
Gene Names: RHO
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Rhodopsin
Find proteins for P02699 (Bos taurus)
Go to Gene View: RHO
Go to UniProtKB:  P02699
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye InstituteUnited States--

Revision History 

  • Version 1.0: 2019-08-21
    Type: Initial release
  • Version 1.1: 2019-10-09
    Type: Data collection, Database references