Crystal structure of Bos taurus opsin regenerated with 6-carbon ring retinal chromophore

Experimental Data Snapshot

  • Resolution: 4.01 Å
  • R-Value Free: 0.357 
  • R-Value Work: 0.314 
  • R-Value Observed: 0.316 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Photocyclic behavior of rhodopsin induced by an atypical isomerization mechanism.

Gulati, S.Jastrzebska, B.Banerjee, S.Placeres, A.L.Miszta, P.Gao, S.Gunderson, K.Tochtrop, G.P.Filipek, S.Katayama, K.Kiser, P.D.Mogi, M.Stewart, P.L.Palczewski, K.

(2017) Proc Natl Acad Sci U S A 114: E2608-E2615

  • DOI: https://doi.org/10.1073/pnas.1617446114
  • Primary Citation of Related Structures:  
    5TE3, 5TE5

  • PubMed Abstract: 

    Vertebrate rhodopsin (Rh) contains 11- cis -retinal as a chromophore to convert light energy into visual signals. On absorption of light, 11- cis -retinal is isomerized to all- trans -retinal, constituting a one-way reaction that activates transducin (G t ) followed by chromophore release. Here we report that bovine Rh, regenerated instead with a six-carbon-ring retinal chromophore featuring a C 11 =C 12 double bond locked in its cis conformation (Rh6mr), employs an atypical isomerization mechanism by converting 11- cis to an 11,13- dicis configuration for prolonged G t activation. Time-dependent UV-vis spectroscopy, HPLC, and molecular mechanics analyses revealed an atypical thermal reisomerization of the 11,13- dicis to the 11- cis configuration on a slow timescale, which enables Rh6mr to function in a photocyclic manner similar to that of microbial Rhs. With this photocyclic behavior, Rh6mr repeatedly recruits and activates G t in response to light stimuli, making it an excellent candidate for optogenetic tools based on retinal analog-bound vertebrate Rhs. Overall, these comprehensive structure-function studies unveil a unique photocyclic mechanism of Rh activation by an 11- cis -to-11,13- dicis isomerization.

  • Organizational Affiliation

    Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rhodopsin349Bos taurusMutation(s): 1 
Membrane Entity: Yes 
Find proteins for P02699 (Bos taurus)
Explore P02699 
Go to UniProtKB:  P02699
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02699
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 7AB

Download Ideal Coordinates CCD File 
B [auth A](2E)-{(4E)-4-[(3E)-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-3-en-2-ylidene]cyclohex-2-en-1-ylidene}acetaldehyde
C21 H28 O
Experimental Data & Validation

Experimental Data

  • Resolution: 4.01 Å
  • R-Value Free: 0.357 
  • R-Value Work: 0.314 
  • R-Value Observed: 0.316 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.725α = 90
b = 81.725β = 90
c = 200.012γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-03-29
    Changes: Database references
  • Version 1.2: 2017-04-05
    Changes: Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description