5TE3

Crystal structure of Bos taurus opsin at 2.7 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1073/pnas.1617446114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Vertebrate rhodopsin (Rh) contains 11- <i>cis </i>-retinal as a chromophore to convert light energy into visual signals. On absorption of light, 11- <i>cis </i>-retinal is isomerized to all- <i>trans </i>-retinal, constituting a one-way reaction that ...

    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

    Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, OH 44106.,Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 00-927 Warsaw, Poland.,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106.,Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106; kxk477@case.edu kxp65@case.edu.,Northeastern Collaborative Access Team, Argonne National Laboratory, Argonne, IL 60439.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850.,Novartis Institutes for BioMedical Research, Cambridge, MA 02139.,Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106.,Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rhodopsin
A
348Bos taurusMutation(s): 0 
Gene Names: RHO
Find proteins for P02699 (Bos taurus)
Go to Gene View: RHO
Go to UniProtKB:  P02699
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PLM
Query on PLM

Download SDF File 
Download CCD File 
A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
BOG
Query on BOG

Download SDF File 
Download CCD File 
A
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.245 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 242.660α = 90.00
b = 242.660β = 90.00
c = 111.770γ = 120.00
Software Package:
Software NamePurpose
REFMACphasing
XDSdata reduction
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-03-29
    Type: Database references
  • Version 1.2: 2017-04-05
    Type: Database references