7ZTQ

Crystal structure of the carotenoid-binding protein domain from silkworm Bombyx mori (BmCBP) in the apoform


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.146 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Silkworm carotenoprotein as an efficient carotenoid extractor, solubilizer and transporter.

Sluchanko, N.N.Slonimskiy, Y.B.Egorkin, N.A.Varfolomeeva, L.A.Faletrov, Y.V.Moysenovich, A.M.Parshina, E.Y.Friedrich, T.Maksimov, E.G.Boyko, K.M.Popov, V.O.

(2022) Int J Biol Macromol 223: 1381-1393

  • DOI: https://doi.org/10.1016/j.ijbiomac.2022.11.093
  • Primary Citation of Related Structures:  
    7ZTQ, 7ZTR, 7ZTU

  • PubMed Abstract: 

    Found in many organisms, water-soluble carotenoproteins are prospective antioxidant nanocarriers for biomedical applications. Yet, the toolkit of characterized carotenoproteins is rather limited: such proteins are either too specific binders of only few different carotenoids, or their ability to transfer carotenoids to various acceptor systems is unknown. Here, by focusing on a recently characterized recombinant ~27-kDa Carotenoid-Binding Protein from Bombyx mori (BmCBP) [Slonimskiy et al., International Journal of Biological Macromolecules 214 (2022): 664-671], we analyze its carotenoid-binding repertoire and potential as a carotenoid delivery module. We show that BmCBP forms productive complexes with both hydroxyl- and ketocarotenoids - lutein, zeaxanthin, astaxanthin, canthaxanthin and a smaller antioxidant, aporhodoxanthinone, but not with β-carotene or retinal, which defines its broad ligand specificity toward xanthophylls valuable to human health. Moreover, the His-tagged BmCBP apoform is capable of cost-efficient and scalable enrichment of xanthophylls from various crude methanolic herbal extracts. Upon carotenoid binding, BmCBP remains monomeric and shows a remarkable ability to dynamically shuttle carotenoids to biological membrane models and to unrelated carotenoproteins, which in particular makes from the cyanobacterial Orange Carotenoid Protein a blue-light controlled photoswitch. Furthermore, administration of BmCBP loaded by zeaxanthin stimulates fibroblast growth, which is attractive for cell- and tissue-based assays.


  • Organizational Affiliation

    A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation. Electronic address: [email protected].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carotenoid-binding protein253Bombyx moriMutation(s): 0 
Gene Names: BmCBP
UniProt
Find proteins for Q8MYA9 (Bombyx mori)
Explore Q8MYA9 
Go to UniProtKB:  Q8MYA9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8MYA9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.146 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.911α = 90
b = 67.326β = 90
c = 121.637γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Higher Education of the Russian FederationRussian Federation075-15-2021-1354
Russian Foundation for Basic ResearchRussian Federation20-54-12018
German Research Foundation (DFG)GermanyFR1276/6-1

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-26
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Refinement description