1H68

sensory rhodopsin II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-Ray Structure of Sensory Rhodopsin II at 2.1 A Resolution

Royant, A.Nollert, P.Edman, K.Neutze, R.Landau, E.M.Pebay-Peyroula, E.Navarro, J.

(2001) Proc.Natl.Acad.Sci.USA 98: 10131

  • DOI: 10.1073/pnas.181203898

  • PubMed Abstract: 
  • Sensory rhodopsins (SRs) belong to a subfamily of heptahelical transmembrane proteins containing a retinal chromophore. These photoreceptors mediate the cascade of vision in animal eyes and phototaxis in archaebacteria and unicellular flagellated alg ...

    Sensory rhodopsins (SRs) belong to a subfamily of heptahelical transmembrane proteins containing a retinal chromophore. These photoreceptors mediate the cascade of vision in animal eyes and phototaxis in archaebacteria and unicellular flagellated algae. Signal transduction by these photoreceptors occurs by means of transducer proteins. The two archaebacterial sensory rhodopsins SRI and SRII are coupled to the membrane-bound HtrI and HtrII transducer proteins. Activation of these proteins initiates phosphorylation cascades that modulate the flagellar motors, resulting in either attractant (SRI) or repellent (SRII) phototaxis. In addition, transducer-free SRI and SRII were shown to operate as proton pumps, analogous to bacteriorhodopsin. Here, we present the x-ray structure of SRII from Natronobacterium pharaonis (pSRII) at 2.1-A resolution, revealing a unique molecular architecture of the retinal-binding pocket. In particular, the structure of pSRII exhibits a largely unbent conformation of the retinal (as compared with bacteriorhodopsin and halorhodopsin), a hydroxyl group of Thr-204 in the vicinity of the Schiff base, and an outward orientation of the guanidinium group of Arg-72. Furthermore, the structure reveals a putative chloride ion that is coupled to the Schiff base by means of a hydrogen-bond network and a unique, positively charged surface patch for a probable interaction with HtrII. The high-resolution structure of pSRII provides a structural basis to elucidate the mechanisms of phototransduction and color tuning.


    Organizational Affiliation

    Institut de Biologie Structurale, Unité Mixte de Recherche 5075 Commissariat à l'Energie Atomique-Centre National de la Recherche Scientifique, Université Joseph Fourier, 41 Rue Jules Horowitz, F-38027 Grenoble Cedex 1, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SENSORY RHODOPSIN II
A
239Natronomonas pharaonisGene Names: sop2 (sopII)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Bacterial and Algal Rhodopsins
Protein: 
Sensory Rhodopsin II (SRII)
Find proteins for P42196 (Natronomonas pharaonis)
Go to UniProtKB:  P42196
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
RET
Query on RET

Download SDF File 
Download CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.237 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 84.830α = 90.00
b = 128.740β = 90.00
c = 50.740γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing
DENZOdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-28
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance