5TE3

Crystal structure of Bos taurus opsin at 2.7 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report



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:  
    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 ...

    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

    Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RhodopsinA348Bos taurusMutation(s): 0 
Gene Names: RHO
Find proteins for P02699 (Bos taurus)
Explore P02699 
Go to UniProtKB:  P02699
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
4 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 242.66α = 90
b = 242.66β = 90
c = 111.77γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary