4EAX

Mouse NGF in complex with Lyso-PS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

wwPDB Validation 3D Report Full Report



Literature

Structural and functional insights into lipid-bound nerve growth factors

Tong, Q.Wang, F.Zhou, H.Z.Sun, H.L.Song, H.Shu, Y.Y.Gong, Y.Zhang, W.T.Cai, T.X.Yang, F.Q.Tang, J.Jiang, T.

(2012) FASEB J 26: 3811-3821

  • DOI: 10.1096/fj.12-207316
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Nerve growth factor (NGF) is a dimeric molecule that modulates the survival, proliferation, and differentiation of nervous cells and is also known to act on cells of the immune system and endocrine system. NGFs extracted from mouse submaxillary gland ...

    Nerve growth factor (NGF) is a dimeric molecule that modulates the survival, proliferation, and differentiation of nervous cells and is also known to act on cells of the immune system and endocrine system. NGFs extracted from mouse submaxillary gland and cobra venom have different immunological behaviors, yet the underlying mechanism remains unclear. Here we report the crystal structure of the NGF purified from Chinese cobra Naja naja atra (cNGF), which unexpectedly reveals a 2-tailed lipid molecule that is embedded between the two protomers of the NGF homodimer. In addition, crystallographic analysis indicated that the purified mouse NGF(mNGF) is free from lipid but can bind lysophosphatidylserine (lyso-PS) in the same pocket as cNGF. Bioassays indicated that the binding of lipid molecules to cNGF and mNGF are essential for their mast cell activation activity and abates their p75(NTR) binding capacity. Taken together, these results suggest a new mechanism for the regulation of the function of NGF.


    Organizational Affiliation

    National Key Laboratory of Biomacromolecules, Institute of Biophysics, Beijing, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-nerve growth factor
A, B, C, D
120Mus musculusMutation(s): 0 
Gene Names: NgfNgfb
Find proteins for P01139 (Mus musculus)
Go to UniProtKB:  P01139
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S12
Query on S12

Download CCD File 
B, D
O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine
C24 H46 N O9 P
JZWNYZVVZXZRRH-VXKWHMMOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.529α = 90
b = 96.529β = 90
c = 163.78γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-03-23 
  • Released Date: 2012-09-12 
  • Deposition Author(s): Jiang, T., Tong, Q.

Revision History 

  • Version 1.0: 2012-09-12
    Type: Initial release