6OFJ | pdb_00006ofj

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

• PDB DOI: https://doi.org/10.2210/pdb6OFJ/pdb
• EM Map EMD-20047: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Bos taurus
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2019-03-30 Released: 2019-08-21 
• Deposition Author(s): Zhao, D.Y., Gulati, S., Ernst, O.P., Palczewski, K.
• Funding Organization(s): National Institutes of Health/National Eye Institute (NIH/NEI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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 Biological Chem 294: 14215-14230

• PubMed: 31399513 
• DOI: https://doi.org/10.1074/jbc.RA119.010089
• Primary Citation Related Structures: 
  6OFJ


• PubMed Abstract: 
  

  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.

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Organizational Affiliation: 
• Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany.
Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697.
Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106.
Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw 02-093, Poland.
Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada [e-mail].
Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697 [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 78.06 kDa 
• Atom Count: 5,168 
• Modeled Residue Count: 650 
• Deposited Residue Count: 696 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodopsin	A, B	348	Bos taurus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P02699 (Bos taurus) Explore P02699  Go to UniProtKB:  P02699

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-08-21 
Deposition Author(s): Zhao, D.Y., Gulati, S., Ernst, O.P., Palczewski, K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Eye Institute (NIH/NEI)	United States	--

Revision History  

• Version 1.0: 2019-08-21
  Type: Initial release
  
• Version 1.1: 2019-10-09
  Changes: Data collection, Database references
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2019-12-18
  Changes: Other
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Structure summary
• Version 1.5: 2025-06-04
  Changes: Data collection