4XPJ | pdb_00004xpj

Crystal structure of Nerve growth factor in complex with lysophosphatidylinositol

• PDB DOI: https://doi.org/10.2210/pdb4XPJ/pdb

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.266 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

The structure of nerve growth factor in complex with lysophosphatidylinositol

Sun, H.L., Jiang, T.

(2015) Acta Crystallogr F Struct Biol Commun 71: 906-912

• PubMed: 26144237 
• DOI: https://doi.org/10.1107/S2053230X15008870
• Primary Citation Related Structures: 
  4XPJ


• 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 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.

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, People's Republic of 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)

Macromolecule Content 

• Total Structure Weight: 27.51 kDa 
• Atom Count: 1,750 
• Modeled Residue Count: 210 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-nerve growth factor	A, B	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
LPY	C [auth B]	(2R)-2-hydroxy-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl tridecanoate C22 H43 O12 P QGSQXOJTKFYHRK-FBYKMOGESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.266 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.689	α = 90
b = 96.689	β = 90
c = 164.339	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2015-07-15
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 1.2: 2024-11-13
  Changes: Structure summary