3DDL

Crystallographic Structure of Xanthorhodopsin, a Light-Driven Ion Pump with Dual Chromophore


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore.

Luecke, H.Schobert, B.Stagno, J.Imasheva, E.S.Wang, J.M.Balashov, S.P.Lanyi, J.K.

(2008) Proc Natl Acad Sci U S A 105: 16561-16565

  • DOI: 10.1073/pnas.0807162105
  • Primary Citation of Related Structures:  
    3DDL

  • PubMed Abstract: 
  • Homologous to bacteriorhodopsin and even more to proteorhodopsin, xanthorhodopsin is a light-driven proton pump that, in addition to retinal, contains a noncovalently bound carotenoid with a function of a light-harvesting antenna. We determined the structure of this eubacterial membrane protein-carotenoid complex by X-ray diffraction, to 1 ...

    Homologous to bacteriorhodopsin and even more to proteorhodopsin, xanthorhodopsin is a light-driven proton pump that, in addition to retinal, contains a noncovalently bound carotenoid with a function of a light-harvesting antenna. We determined the structure of this eubacterial membrane protein-carotenoid complex by X-ray diffraction, to 1.9-A resolution. Although it contains 7 transmembrane helices like bacteriorhodopsin and archaerhodopsin, the structure of xanthorhodopsin is considerably different from the 2 archaeal proteins. The crystallographic model for this rhodopsin introduces structural motifs for proton transfer during the reaction cycle, particularly for proton release, that are dramatically different from those in other retinal-based transmembrane pumps. Further, it contains a histidine-aspartate complex for regulating the pK(a) of the primary proton acceptor not present in archaeal pumps but apparently conserved in eubacterial pumps. In addition to aiding elucidation of a more general proton transfer mechanism for light-driven energy transducers, the structure defines also the geometry of the carotenoid and the retinal. The close approach of the 2 polyenes at their ring ends explains why the efficiency of the excited-state energy transfer is as high as approximately 45%, and the 46 degrees angle between them suggests that the chromophore location is a compromise between optimal capture of light of all polarization angles and excited-state energy transfer.


    Organizational Affiliation

    Departments of Molecular Biology and Biochemistry, and Physiology and Biophysics, and Center for Biomembrane Systems, University of California, Irvine, CA 92697.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Xanthorhodopsin AB273Salinibacter ruberMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Bacterial, Algal, Viral, and Unusual Rhodopsins
Protein: 
Xanthorhodopsin
Find proteins for Q2S2F8 (Salinibacter ruber (strain DSM 13855 / M31))
Explore Q2S2F8 
Go to UniProtKB:  Q2S2F8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SXN
Query on SXN

Download Ideal Coordinates CCD File 
A, B
Salinixanthin
C61 H92 O9
BUNXUZXQWPTVHM-CRAPJSHNSA-N
 Ligand Interaction
PCW
Query on PCW

Download Ideal Coordinates CCD File 
B
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
 Ligand Interaction
PX4
Query on PX4

Download Ideal Coordinates CCD File 
B
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O
 Ligand Interaction
RET
Query on RET

Download Ideal Coordinates CCD File 
A, B
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
UNL
Query on UNL

Download Ideal Coordinates CCD File 
A, B
Unknown ligand
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.247 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.74α = 76.35
b = 59.49β = 74.93
c = 59.72γ = 64.08
Software Package:
Software NamePurpose
d*TREKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
d*TREKdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2016-06-08
    Changes: Atomic model