3IJ2

Ligand-receptor structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.75 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular and structural insight into proNGF engagement of p75NTR and sortilin.

Feng, D.Kim, T.Ozkan, E.Light, M.Torkin, R.Teng, K.K.Hempstead, B.L.Garcia, K.C.

(2010) J Mol Biol 396: 967-984

  • DOI: 10.1016/j.jmb.2009.12.030
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Nerve growth factor (NGF) is initially synthesized as a precursor, proNGF, that is cleaved to release its C-terminal mature form. Recent studies suggested that proNGF is not an inactive precursor but acts as a signaling ligand distinct from its matur ...

    Nerve growth factor (NGF) is initially synthesized as a precursor, proNGF, that is cleaved to release its C-terminal mature form. Recent studies suggested that proNGF is not an inactive precursor but acts as a signaling ligand distinct from its mature counterpart. proNGF and mature NGF initiate opposing biological responses by utilizing both distinct and shared receptor components. In this study, we carried out structural and biochemical characterization of proNGF interactions with p75NTR and sortilin. We crystallized proNGF complexed to p75NTR and present the structure at 3.75-A resolution. The structure reveals a 2:2 symmetric binding mode, as compared with the asymmetric structure of a previously reported crystal structure of mature NGF complexed to p75NTR and the 2:2 symmetric complex of neurotrophin-3 (NT-3) and p75NTR. Here, we discuss the possible origins and implications of the different stoichiometries. In the proNGF-p75NTR complex, the pro regions of proNGF are mostly disordered and two hairpin loops (loop 2) at the top of the NGF dimer have undergone conformational changes in comparison with mature NT structures, suggesting possible interactions with the propeptide. We further explored the binding characteristics of proNGF to sortilin using surface plasmon resonance and cell-based assays and determined that calcium ions promote the formation of a stable ternary complex of proNGF-sortilin-p75NTR. These results, together with those of previous structural and mechanistic studies of NT-receptor interactions, suggest the potential for distinct signaling activities through p75NTR mediated by different NT-induced conformational changes.


    Organizational Affiliation

    Department of Cellular and Molecular Physiology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-nerve growth factor
A, B
230Mus musculusMutation(s): 8 
Gene Names: NgfNgfb
Find proteins for P01139 (Mus musculus)
Go to UniProtKB:  P01139
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nerve growth factor receptor (TNFR superfamily, member 16)
X, Y
171Rattus norvegicusMutation(s): 1 
Gene Names: NgfrRP23-67E18.6-001Tnfrsf16
Find proteins for P07174 (Rattus norvegicus)
Go to UniProtKB:  P07174
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.75 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.257 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.406α = 90
b = 145.406β = 90
c = 114.252γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-08-03 
  • Released Date: 2010-01-12 
  • Deposition Author(s): Feng, D., Garcia, K.C.

Revision History 

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description