6IWN

Structural insight into probable lipid transfer mechanism of non-specific lipid transfer protein via intermediate structures in Solanum melongena


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.408 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into the lipid transfer mechanism of a non-specific lipid transfer protein.

Madni, Z.K.Tripathi, S.K.Salunke, D.M.

(2019) Plant J. --: --

  • DOI: 10.1111/tpj.14627
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The non-specific lipid transfer proteins (nsLTPs) are multifunctional seed proteins engaged in several different physiological processes. The nsLTPs are stabilized by four disulfide bonds and exhibit a characteristic hydrophobic cavity, which is the ...

    The non-specific lipid transfer proteins (nsLTPs) are multifunctional seed proteins engaged in several different physiological processes. The nsLTPs are stabilized by four disulfide bonds and exhibit a characteristic hydrophobic cavity, which is the primary lipid binding site. While these proteins are known to transfer lipids between membranes, the mechanism of lipid transfer has remained elusive. Four crystal structures of nsLTP from S. melongena, one in the apo-state and three myristic acid bound states were determined. Among the three lipid bound states, two lipid molecules were bound on the nsLTP surface at different positions and one was inside the cavity. The lipid dependent conformational changes leading to opening of the cavity were revealed based on structural and spectroscopic data. The surface bound lipid represented a transient intermediate state and the lipid ultimately moved inside the cavity through the cavity gate as revealed by molecular dynamics simulations. Two critical residues in the loop regions played possible 'gating' role in the opening and closing of the cavity. Anti-fungal activity and membrane permeabilization effect of nsLTP against Fusarium oxysporum suggested that it could possibly involve in bleaching out the lipids. Collectively, these studies support a model of lipid transfer mechanism by nsLTP via intermediate states.


    Organizational Affiliation

    International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.,Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, 121001, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Non-specific lipid-transfer protein
A, B
92Solanum melongenaMutation(s): 0 
Find proteins for A0A247D6Y2 (Solanum melongena)
Go to UniProtKB:  A0A247D6Y2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR

Download SDF File 
Download CCD File 
A, B
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, B
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.408 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.225 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 86.349α = 90.00
b = 86.349β = 90.00
c = 50.440γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2019-12-25
    Type: Database references