1TUK

Crystal structure of liganded type 2 non specific lipid transfer protein from wheat


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of a liganded type 2 non-specific lipid-transfer protein from wheat and the molecular basis of lipid binding.

Hoh, F.Pons, J.L.Gautier, M.F.de Lamotte, F.Dumas, C.

(2005) Acta Crystallogr.,Sect.D 61: 397-406

  • DOI: 10.1107/S0907444905000417

  • PubMed Abstract: 
  • In plants, a family of ubiquitous proteins named non-specific lipid-transfer proteins (ns-LTPs) facilitates the transfer of fatty acids, phospholipids and steroids between membranes. Recent data suggest that these secreted proteins play a key role in ...

    In plants, a family of ubiquitous proteins named non-specific lipid-transfer proteins (ns-LTPs) facilitates the transfer of fatty acids, phospholipids and steroids between membranes. Recent data suggest that these secreted proteins play a key role in the formation of cuticular wax layers and in defence mechanisms against pathogens. In this study, X-ray crystallography has been used to examine the structural details of the interaction between a wheat type 2 ns-LTP and a lipid, L-alpha-palmitoyl-phosphatidyl glycerol. This crystal structure was solved ab initio at 1.12 A resolution by direct methods. The typical alpha-helical bundle fold of this protein is maintained by four disulfide bridges and delineates two hydrophobic cavities. The inner surface of the main cavity is lined by non-polar residues that provide a hydrophobic environment for the palmitoyl moiety of the lipid. The head-group region of this lipid protrudes from the surface and makes several polar interactions with a conserved patch of basic residues at the entrance of the pocket. The alkyl chain of a second lipid is bound within an adjacent smaller cavity. The structure shows that binding of the lipid tails to the protein involves extensive hydrophobic interactions.


    Related Citations: 
    • Refined solution structure of a liganded type 2 wheat nonspecific lipid transfer protein
      Pons, J.L.,de Lamotte, F.,Gautier, M.F.,Delsuc, M.A.
      (2003) J.BIOL.CHEM. 278: 14249


    Organizational Affiliation

    Centre de Biochimie Structurale, CNRS UMR5048-INSERM U554, 29 Rue de Navacelles, 34090 Montpellier, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nonspecific lipid-transfer protein 2G
A
67Triticum aestivumMutation(s): 0 
Find proteins for P82900 (Triticum aestivum)
Go to UniProtKB:  P82900
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
PGM
Query on PGM

Download SDF File 
Download CCD File 
A
1-MYRISTOYL-2-HYDROXY-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)]
LYSOPHOSPHATIDYLGLYCEROL
C22 H44 O9 P
BVJSKAUUFXBDOB-SFTDATJTSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.137 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 61.465α = 90.00
b = 29.320β = 127.65
c = 41.550γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
REFMACrefinement
SnBphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2016-12-28
    Type: Structure summary
  • Version 1.4: 2017-10-11
    Type: Refinement description