5TVI

Crystal structure of non-specific lipid transfer protein reveals non-canonical lipid binding: possible relevance in modulating allergenicity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of nonspecific lipid transfer protein from Solanum melongena

Jain, A.Salunke, D.M.

(2017) Proteins 85: 1820-1830

  • DOI: 10.1002/prot.25335
  • Primary Citation of Related Structures:  
    5TVI

  • PubMed Abstract: 
  • Lipids are considered to protect protein allergens from proteolysis and are generally seen to exist in a bound form. One of the well-known plant protein families with bound lipids is non-specific lipid transfer proteins (nsLTPs). Structure-function r ...

    Lipids are considered to protect protein allergens from proteolysis and are generally seen to exist in a bound form. One of the well-known plant protein families with bound lipids is non-specific lipid transfer proteins (nsLTPs). Structure-function relationships in the case of the members of non-specific lipid transfer protein family are not clearly understood. As part of exploring the seed proteome, we have analyzed the proteome of a member of Solanaceae family, Solanum melongena (eggplant) and a non-specific lipid transfer protein from S. melongena, SM80.2 was purified, crystallized and the structure was determined at 1.87 Å resolution. Overall, the tertiary structure is a cluster of α-helices forming an internal hydrophobic cavity. Absence of conserved Tyr79, known to govern the plasticity of hydrophobic cavity, and formation of hydrogen bond between Asn79 and Asn36 further reduced the pocket size. Structural analysis of SM80.2 thus gives insight about a new hydrogen bond mediated mechanism followed in closure of the binding pocket. Extra electron densities observed at two different places on the protein surface and not in the cavity could provide interesting physiological relevance. In light of allergenic properties, probably overlapping of epitopic region and ligand binding on surface could be a main reason. This work shows first crystal structure of A-like nsLTP with a close binding pocket and extra density on the surface suggesting a plausible intermediate state during transfer.


    Organizational Affiliation

    International Centre for Genetic Engineering and Biotechnology, Structural Immunology Lab, New Delhi, 110067, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
non specific lipid transfer proteinVW92Solanum melongenaMutation(s): 0 
Find proteins for A0A247D6Y2 (Solanum melongena)
Explore A0A247D6Y2 
Go to UniProtKB:  A0A247D6Y2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
O8N
Query on O8N

Download CCD File 
W
octacosan-1-ol
C28 H58 O
CNNRPFQICPFDPO-UHFFFAOYSA-N
 Ligand Interaction
MYR
Query on MYR

Download CCD File 
V
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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V
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.188 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.48α = 90
b = 87.48β = 90
c = 49.67γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHENIXphasing
iMOSFLMdata processing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Database references