9WM8 | pdb_00009wm8

The crystal structure of AstaP-pink1 from a microalga


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.220 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


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Literature

Structural basis for spectral red shift and UVA absorption in the microalgal water-soluble astaxanthin-binding protein AstaP-pink1.

Mitsui, T.Shomura, Y.Furubayashi, M.Kato, R.Takaichi, S.Kawasaki, S.

(2026) J Struct Biol 218: 108288-108288

  • DOI: https://doi.org/10.1016/j.jsb.2026.108288
  • Primary Citation Related Structures: 
    9WM8

  • PubMed Abstract: 

    AstaPs are water-soluble, photooxidative stress-inducible astaxanthin (AXT)-binding proteins found only in Scenedesmaceae microalgae, where they play a central role in survival under severe photooxidative stress. Here, we focused on the unique function of AstaP-pink1, which converts orange AXT into a pink form and generates a UVA absorption spectrum upon protein binding. AstaP-pink1 was expressed in genetically engineered Escherichia coli strains capable of synthesizing AXT. The host strain harboring pAC-Asta produced adonixanthin, AXT, and zeaxanthin in an approximate ratio of 5:3:2, whereas the strain carrying pMF573 predominantly produced AXT (∼90 % of total carotenoid). Co-expression of the gene encoding AstaP-pink1 in these strains resulted in moderate and selective AXT binding, accompanied by a spectral red shift and UVA absorption, thereby generating pink coloration. Crystal structure analysis of AXT-bound recombinant AstaP-pink1 (rAstaP-pink1) revealed both similarities and differences in AXT binding compared with rAstaP-orange1. Density functional theory (DFT) calculations based on the crystal structure suggested that the larger red shift than that of AstaP-orange1 and the distinct UVA absorption are derived from the conformation of AXT that is compelled by binding to AstaP-pink1. This study suggests that AXT binding by AstaP-pink1 not only facilitates the water solubilization of AXT but also generates the observed spectral properties.


  • Organizational Affiliation
    • Department of Molecular Microbiology, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan.

Macromolecule Content 

  • Total Structure Weight: 20.55 kDa 
  • Atom Count: 1,447 
  • Modeled Residue Count: 163 
  • Deposited Residue Count: 191 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AstaP-pink1191Scenedesmaceae sp.Mutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AXT
(Subject of Investigation/LOI)

Query on AXT



Download:Ideal Coordinates CCD File
B [auth A]ASTAXANTHIN
C40 H52 O4
MQZIGYBFDRPAKN-UWFIBFSHSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.845α = 90
b = 52.629β = 90
c = 71.37γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP25ama121001
Japan Society for the Promotion of Science (JSPS)JapanJP24H02093

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-22
    Type: Initial release