7ZVR

Crystal structure of the carotenoid-binding protein domain from silkworm Bombyx mori (BmCBP) complexed with zeaxanthin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural basis for the carotenoid binding and transport function of a START domain.

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

(2022) Structure 30: 1647

  • DOI: https://doi.org/10.1016/j.str.2022.10.007
  • Primary Citation of Related Structures:  
    7ZVQ, 7ZVR

  • PubMed Abstract: 

    STARD3, a steroidogenic acute regulatory lipid transfer protein, was identified as a key xanthophyll-binding protein in the human retina. STARD3 and its homologs in invertebrates are known to bind and transport carotenoids, but this lacks structural elucidation. Here, we report high-resolution crystal structures of the apo- and zeaxanthin (ZEA)-bound carotenoid-binding protein from silkworm Bombyx mori (BmCBP). Having a STARD3-like fold, BmCBP features novel elements, including the Ω1-loop that, in the apoform, is uniquely fixed on the α4-helix by an R173-D279 salt bridge. We exploit absorbance, Raman and dichroism spectroscopy, and calorimetry to describe how ZEA and BmCBP mutually affect each other in the complex. We identify key carotenoid-binding residues, confirm their roles by ZEA-binding capacity and X-ray structures of BmCBP mutants, and also demonstrate that markedly different carotenoid-binding capacities of BmCBP and human STARD3 stem from differences in the structural organization of their carotenoid-binding cavity.


  • Organizational Affiliation

    A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 33 Leninsky Prospect, Building 1, Moscow 119071, Russian Federation. Electronic address: nikolai.sluchanko@mail.ru.


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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZEX (Subject of Investigation/LOI)
Query on ZEX

Download Ideal Coordinates CCD File 
B [auth A](1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol
C40 H56 O2
YRMDXLDAZBQLBK-WIHRHFSMSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.688α = 90
b = 66.528β = 90
c = 120.516γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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: 2022-11-23
    Changes: Database references
  • Version 1.2: 2022-12-14
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description