4XPJ

Crystal structure of Nerve growth factor in complex with lysophosphatidylinositol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.605 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The structure of nerve growth factor in complex with lysophosphatidylinositol

Sun, H.L.Jiang, T.

(2015) Acta Crystallogr.,Sect.F 71: 906-912

  • DOI: 10.1107/S2053230X15008870

  • PubMed Abstract: 
  • Nerve growth factor (NGF) is an important protein that is involved in a variety of physiological processes in cell survival, differentiation, proliferation and maintenance. The previously reported crystal structure of mouse NGF (mNGF) in complex with ...

    Nerve growth factor (NGF) is an important protein that is involved in a variety of physiological processes in cell survival, differentiation, proliferation and maintenance. The previously reported crystal structure of mouse NGF (mNGF) in complex with lysophosphatidylserine (LysoPS) showed that mNGF can bind LysoPS at its dimeric interface. To expand the understanding of the structural basis for specific lipid recognition by NGF, the crystal structure of mNGF complexed with lysophosphatidylinositol (13:0 LysoPI) was solved. Interestingly, in addition to Lys88, which interacts with the head glycerol group and the phosphate group of LysoPI, as seen in the mNGF-LysoPS structure, two additional residues, Tyr52 and Arg50, were found to assist in lipid binding by forming hydrogen bonds to the inositol moiety of the LysoPI molecule. The results suggest a specific recognition mechanism of inositol group-containing lipids by NGF, which may help in the design of bioactive compounds that can be delivered by NGF.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-nerve growth factor
A, B
120Mus musculusMutation(s): 0 
Gene Names: Ngf (Ngfb)
Find proteins for P01139 (Mus musculus)
Go to UniProtKB:  P01139
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LPY
Query on LPY

Download SDF File 
Download CCD File 
B
(2R)-2-hydroxy-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl tridecanoate
sn-1-tridecanoyl-phosphatidylinositol
C22 H43 O12 P
QGSQXOJTKFYHRK-FBYKMOGESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.605 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.195 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 96.689α = 90.00
b = 96.689β = 90.00
c = 164.339γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data processing
PHENIXrefinement
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-01-17 
  • Released Date: 2015-07-15 
  • Deposition Author(s): Sun, H.L., Jiang, T.

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release