3E8T | pdb_00003e8t

Crystal Structure of Epiphyas postvittana Takeout 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.182 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.142 (Depositor), 0.141 (DCC) 
  • R-Value Observed: 
    0.144 (Depositor) 

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This is version 1.2 of the entry. See complete history

Literature

Crystal structure of Epiphyas postvittana takeout 1 with bound ubiquinone supports a role as ligand carriers for takeout proteins in insects

Hamiaux, C.Stanley, D.Greenwood, D.R.Baker, E.N.Newcomb, R.D.

(2009) J Biological Chem 284: 3496-3503

  • DOI: https://doi.org/10.1074/jbc.M807467200
  • Primary Citation Related Structures: 
    3E8T, 3E8W

  • PubMed Abstract: 

    Takeout (To) proteins are found exclusively in insects and have been proposed to have important roles in various aspects of their physiology and behavior. Limited sequence similarity with juvenile hormone-binding proteins (JHBPs), which specifically bind and transport juvenile hormones in Lepidoptera, suggested a role for To proteins in binding hydrophobic ligands. We present the first crystal structure of a To protein, EpTo1 from the light brown apple moth Epiphyas postvittana, solved in-house by the single-wavelength anomalous diffraction technique using sulfur anomalous dispersion, and refined to 1.3 angstroms resolution. EpTo1 adopts the unusual alpha/beta-wrap fold, seen only for JHBP and several mammalian lipid carrier proteins, a scaffold tailored for the binding and/or transport of hydrophobic ligands. EpTo1 has a 45 angstroms long, purely hydrophobic, internal tunnel that extends for the full length of the protein and accommodates a bound ligand. The latter was shown by mass spectrometry to be ubiquinone-8 and is probably derived from Escherichia coli. The structure provides the first direct experimental evidence that To proteins are ligand carriers; gives insights into the nature of endogenous ligand(s) of EpTo1; shows, by comparison with JHBP, a basis for different ligand specificities; and suggests a mechanism for the binding/release of ligands.


  • Organizational Affiliation
    • The Horticulture and Food Research Institute of New Zealand Limited (HortResearch), Private Bag 92169, Auckland 1142, New Zealand.

Macromolecule Content 

  • Total Structure Weight: 25.24 kDa 
  • Atom Count: 2,145 
  • Modeled Residue Count: 216 
  • Deposited Residue Count: 220 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Takeout-like protein 1220Epiphyas postvittanaMutation(s): 0 
Gene Names: takeout-like 1
UniProt
Find proteins for B5ABT1 (Epiphyas postvittana)
Explore B5ABT1 
Go to UniProtKB:  B5ABT1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5ABT1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UQ8

Query on UQ8



Download:Ideal Coordinates CCD File
B [auth A]Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.182 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.142 (Depositor), 0.141 (DCC) 
  • R-Value Observed: 0.144 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.454α = 90
b = 45.178β = 108.84
c = 53.778γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary