7EKR

The crystal structure of Orange carotenoid binding protein 1 (OCP1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Color-Tuning Mechanism of the Lit Form of Orange Carotenoid Protein.

Han, M.H.Yang, H.W.Yoon, J.Villafani, Y.Song, J.Y.Pan, C.H.Park, K.Cho, Y.Song, J.J.Kim, S.J.Park, Y.I.Park, J.

(2023) Mol Cells 46: 513-525

  • DOI: https://doi.org/10.14348/molcells.2023.2186
  • Primary Citation of Related Structures:  
    7EKR

  • PubMed Abstract: 

    Orange carotenoid protein (OCP) of photosynthetic cyanobacteria binds to ketocarotenoids noncovalently and absorbs excess light to protect the host organism from light-induced oxidative damage. Herein, we found that mutating valine 40 in the α3 helix of Gloeocapsa sp. PCC 7513 (G l OCP1) resulted in blue- or red-shifts of 6-20 nm in the absorption maxima of the lit forms. We analyzed the origins of absorption maxima shifts by integrating X-ray crystallography, homology modeling, molecular dynamics simulations, and hybrid quantum mechanics/molecular mechanics calculations. Our analysis suggested that the single residue mutations alter the polar environment surrounding the bound canthaxanthin, thereby modulating the degree of charge transfer in the photoexcited state of the chromophore. Our integrated investigations reveal the mechanism of color adaptation specific to OCPs and suggest a design principle for color-specific photoswitches.


  • Organizational Affiliation

    Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orange carotenoid protein
A, B
355Gloeocapsa sp. PCC 7513Mutation(s): 0 
Gene Names: opc1
UniProt
Find proteins for A0A7M3UF22 (Gloeocapsa sp. PCC 7513)
Explore A0A7M3UF22 
Go to UniProtKB:  A0A7M3UF22
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7M3UF22
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.944α = 90
b = 82.944β = 90
c = 197.638γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-13
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-29
    Changes: Refinement description