7YTB

Crystal structure of Kin4B8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Phototrophy by antenna-containing rhodopsin pumps in aquatic environments.

Chazan, A.Das, I.Fujiwara, T.Murakoshi, S.Rozenberg, A.Molina-Marquez, A.Sano, F.K.Tanaka, T.Gomez-Villegas, P.Larom, S.Pushkarev, A.Malakar, P.Hasegawa, M.Tsukamoto, Y.Ishizuka, T.Konno, M.Nagata, T.Mizuno, Y.Katayama, K.Abe-Yoshizumi, R.Ruhman, S.Inoue, K.Kandori, H.Leon, R.Shihoya, W.Yoshizawa, S.Sheves, M.Nureki, O.Beja, O.

(2023) Nature 615: 535-540

  • DOI: https://doi.org/10.1038/s41586-023-05774-6
  • Primary Citation of Related Structures:  
    7YTB, 8I2Z

  • PubMed Abstract: 

    Energy transfer from light-harvesting ketocarotenoids to the light-driven proton pump xanthorhodopsins has been previously demonstrated in two unique cases: an extreme halophilic bacterium 1 and a terrestrial cyanobacterium 2 . Attempts to find carotenoids that bind and transfer energy to abundant rhodopsin proton pumps 3 from marine photoheterotrophs have thus far failed 4-6 . Here we detected light energy transfer from the widespread hydroxylated carotenoids zeaxanthin and lutein to the retinal moiety of xanthorhodopsins and proteorhodopsins using functional metagenomics combined with chromophore extraction from the environment. The light-harvesting carotenoids transfer up to 42% of the harvested energy in the violet- or blue-light range to the green-light absorbing retinal chromophore. Our data suggest that these antennas may have a substantial effect on rhodopsin phototrophy in the world's lakes, seas and oceans. However, the functional implications of our findings are yet to be discovered.


  • Organizational Affiliation

    Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kin4B8
A, B
262BdellovibrioMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A977XLG0 (uncultured Bdellovibrionales bacterium)
Explore A0A977XLG0 
Go to UniProtKB:  A0A977XLG0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A977XLG0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.03α = 90
b = 100.03β = 90
c = 116.26γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-15
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references