4EAX | pdb_00004eax

Mouse NGF in complex with Lyso-PS

• PDB DOI: https://doi.org/10.2210/pdb4EAX/pdb

• Classification: HORMONE
• Organism(s): Mus musculus
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

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

• PubMed: 22649032 
• DOI: https://doi.org/10.1096/fj.12-207316
• Primary Citation Related Structures: 
  4EAX, 4EC7


• 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 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.

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Organizational Affiliation: 
• National Key Laboratory of Biomacromolecules, Institute of Biophysics, Beijing, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.01 kDa 
• Atom Count: 3,498 
• Modeled Residue Count: 432 
• Deposited Residue Count: 480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-nerve growth factor	A, B, C, D	120	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01139 (Mus musculus) Explore P01139  Go to UniProtKB:  P01139

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S12	E [auth B], F [auth D]	O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine C24 H46 N O9 P JZWNYZVVZXZRRH-VXKWHMMOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.529	α = 90
b = 96.529	β = 90
c = 163.78	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2012-09-12
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary