9INK | pdb_00009ink

Crystal structure of beta-carotene-binding protein (BBP) from Schistocerca gregaria complexed with beta-carotene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.278 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: in silico
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Literature

Structural basis of selective beta-carotene binding by a soluble protein.

Egorkin, N.A.Dominnik, E.E.Raevskii, R.I.Kuklina, D.D.Varfolomeeva, L.A.Popov, V.O.Boyko, K.M.Sluchanko, N.N.

(2024) Structure 32: 2123-2133.e3

  • DOI: https://doi.org/10.1016/j.str.2024.09.014
  • Primary Citation Related Structures: 
    9INK

  • PubMed Abstract: 

    β-carotene (BCR) is the most abundant carotenoid, a colorant, antioxidant, and provitamin A. The extreme hydrophobicity of this hydrocarbon requires special mechanisms for distribution in aqueous media, including water-soluble carotenoproteins. However, all known carotenoproteins prefer oxygenated carotenoids and bind BCR inefficiently. Here, we present the crystal structure of the BCR-binding protein (BBP) from gregarious male locusts, which is responsible for their vivid yellow body coloration, in complex with its natural ligand, BCR. BBP forms an antiparallel tubular homodimer with α/β-wrap folded monomers, each forming a hydrophobic 47 Å long, coaxial tunnel that opens outward and is occupied by one s-cis C6-C7 , all-trans BCR molecule. In the BCR absence, BBP accepts a range of xanthophylls, with reduced efficiency depending on the position and number of oxygen atoms, but rejects lycopene. The structure captures a pigment complex with a Takeout 1 protein and inspires potential applications of BBP as a BCR solubilizer.


  • Organizational Affiliation
    • A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, 33 Leninsky prospect, building 1, Moscow 119071, Russia; M.V. Lomonosov Moscow State University, School of Biology, 1 Lenin Hills, building 12, Moscow 119991, Russia.

Macromolecule Content 

  • Total Structure Weight: 53.55 kDa 
  • Atom Count: 3,274 
  • Modeled Residue Count: 441 
  • Deposited Residue Count: 510 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Yellow protein of the takeout family
A, B
255Schistocerca gregariaMutation(s): 0 
Gene Names: YPT
UniProt
Find proteins for A0A6N3ISN1 (Schistocerca gregaria)
Explore A0A6N3ISN1 
Go to UniProtKB:  A0A6N3ISN1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6N3ISN1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.278 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.39α = 90
b = 75.51β = 90
c = 224.22γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary
  • Version 1.2: 2024-12-18
    Changes: Database references