X-ray Crystallographic structure of Gloeobacter rhodopsin

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.230 

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X-ray Crystallographic Structure and Oligomerization of Gloeobacter Rhodopsin.

Morizumi, T.Ou, W.L.Van Eps, N.Inoue, K.Kandori, H.Brown, L.S.Ernst, O.P.

(2019) Sci Rep 9: 11283-11283

  • DOI: https://doi.org/10.1038/s41598-019-47445-5
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Gloeobacter rhodopsin (GR) is a cyanobacterial proton pump which can be potentially applied to optogenetics. We solved the crystal structure of GR and found that it has overall similarity to the homologous proton pump from Salinibacter ruber, xanthorhodopsin (XR). We identified distinct structural characteristics of GR's hydrogen bonding network in the transmembrane domain as well as the displacement of extracellular sides of the transmembrane helices relative to those of XR. Employing Raman spectroscopy and flash-photolysis, we found that GR in the crystals exists in a state which displays retinal conformation and photochemical cycle similar to the functional form observed in lipids. Based on the crystal structure of GR, we selected a site for spin labeling to determine GR's oligomerization state using double electron-electron resonance (DEER) spectroscopy and demonstrated the pH-dependent pentamer formation of GR. Determination of the structure of GR as well as its pentamerizing propensity enabled us to reveal the role of structural motifs (extended helices, 3-omega motif and flipped B-C loop) commonly found among light-driven bacterial pumps in oligomer formation. Here we propose a new concept to classify these pumps based on the relationship between their oligomerization propensities and these structural determinants.

  • Organizational Affiliation

    Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gll0198 protein298Gloeobacter violaceus PCC 7421Mutation(s): 0 
Gene Names: gll0198
Membrane Entity: Yes 
Find proteins for Q7NP59 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
Explore Q7NP59 
Go to UniProtKB:  Q7NP59
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7NP59
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.230 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.25α = 90
b = 129.25β = 90
c = 82.65γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other governmentCanadaCanada Excellence Research Chair

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description